ropensci / rsnps

Wrapper to a number of SNP web APIs

rsnps

This package gives you access to data from OpenSNP and NCBI’s dbSNP SNP database.

NOTE

rsnps used to be ropensnp

Data sources

This set of functions/package accesses data from:

• openSNP.org
  • https://opensnp.org
  • See documentation on the openSNP API https://opensnp.org/faq#api
  • See blog post about their API https://opensnp.wordpress.com/2012/01/18/some-progress-on-the-api-json-endpoints/
  • Relevant functions:
    • allgensnp(), allphenotypes(), annotations(), download_users(), fetch_genotypes(), genotypes(), phenotypes(), phenotypes_byid(), users()
• NCBI’s dbSNP SNP database
  • See https://www.ncbi.nlm.nih.gov/snp/ for more details
  • Relevant function:
    • ncbi_snp_query()

Install

Install from CRAN

install.packages("rsnps")

Or dev version

install.packages("remotes")
remotes::install_github("ropensci/rsnps")

library("rsnps")

Usage

NCBI dbSNP data

snps <- c("rs332", "rs420358", "rs1837253", "rs1209415715", "rs111068718")
ncbi_snp_query(snps)

#> # A tibble: 4 × 16
#>   query        chromosome        bp class rsid    gene  alleles ancestral_allele
#>   <chr>        <chr>          <dbl> <chr> <chr>   <chr> <chr>   <chr>           
#> 1 rs332        7          117559593 del   rs1219… "CFT… TTT, d… TTT             
#> 2 rs420358     1           40341239 snv   rs4203… ""    A,C,G,T A               
#> 3 rs1837253    5          111066174 snv   rs1837… ""    T,C     T               
#> 4 rs1209415715 9           41782316 snv   rs1209… ""    T,A,C   T               
#> # ℹ 8 more variables: variation_allele <chr>, seqname <chr>, hgvs <chr>,
#> #   assembly <chr>, ref_seq <chr>, minor <chr>, maf <dbl>,
#> #   maf_population <list>

The ncbi_snp_query() function can be used with an NCBI API which gives access higher numbers of API requests per second. More information about setting this up can be found in the package help accessed via ?rsnps.

openSNP data

genotypes() function

genotypes('rs9939609', userid='1,6,8', df=TRUE)

#>    snp_name snp_chromosome snp_position                 user_name user_id
#> 1 rs9939609             16     53786615 Bastian Greshake Tzovaras       1
#> 2 rs9939609             16     53786615              Nash Parovoz       6
#> 3 rs9939609             16     53786615         Samantha B. Clark       8
#>   genotype_id genotype
#> 1           9       AT
#> 2           5       AT
#> 3           2       TT

phenotypes() function

out <- phenotypes(userid=1)
out$phenotypes$`Hair Type`

#> $phenotype_id
#> [1] 16
#> 
#> $variation
#> [1] "straight"

For more detail, see the vignette: rsnps tutorial.

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for rsnsps in R doing citation(package = 'rsnps')
• Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

rsnps's Issues

Fast query of NCBI's dbSNP?

I have a vector of SNP names of length ~530,000 (which corresponds to an Affymetrix 500K chip).

Using NCBI_snp_query on the first 500 SNPs takes ~70 seconds which would require ~20 hours to query all SNPs.
Surprisingly, NCBI_snp_query2 takes only ~20 seconds, yet querying more information (a slot data, that I'm not interested in).

I wonder

• if there is a way to get a faster query by explicitly saying that my SNPs are ordered (by chromosome and physical position),
• if there is a way to not querying the slot data with NCBI_snp_query2 with the hope of making the query faster,
• if there is a way to query infos on all SNPs that are known to be part of a particular GeneChip (such as Affymetrix 500K).

Tests for NCBI_snp_query

Ensembl fxn for SNP data at some point?

API at http://grch37.rest.ensembl.org/

Get ancestral allele in NCBI_snp_query

my_anc <- tryCatch(my_list$Sequence$.attrs["ancestralAllele"])

credit Margaret Mackinnon

Error in ncbi_snp_query2(proxy_SNPs) : Request-URI Too Long (HTTP 414)

> library(rsnps)
> 
> snps <- c("rs10069690", "rs1011970", "rs1017226", "rs10411161", "rs1045485", "rs10472076",
 "rs10484919", "rs10510333", "rs1053338", "rs10759243", "rs10771399", "rs1078806", "rs10816625", 
"rs10822013", "rs1092913", "rs10941679", "rs10995190", "rs11075884", "rs11075995", "rs11196174", 
"rs11196175", "rs11199914", "rs11205227", "rs11242675", "rs11249433", "rs11552449", "rs11571833", 
"rs11627032", "rs11780156", "rs11814448", "rs11820646", "rs11878583", "rs12048493", "rs1219648", 
"rs12405132", "rs12422552", "rs12443621", "rs12493607")
> 
> ld_search(snps,dataset = "onekgpilot", panel = "CEU", RSquaredLimit = 0.8, distanceLimit = 500, GeneCruiser = TRUE)
Querying SNAP...
Querying NCBI for up-to-date SNP annotation information...
Error in ncbi_snp_query2(proxy_SNPs) : Request-URI Too Long (HTTP 414). In addition: Warning messages:
1: rs11571833	WARNING	Query snp not in 1000GenomesPilot1 
2: rs11571833	WARNING	No matching proxy snps found 
3: rs12048493	WARNING	Query snp not in 1000GenomesPilot1 
4: rs12048493	WARNING	No matching proxy snps found 
> warnings()
Warning messages:
1: rs11571833	WARNING	Query snp not in 1000GenomesPilot1
2: rs11571833	WARNING	No matching proxy snps found
3: rs12048493	WARNING	Query snp not in 1000GenomesPilot1
4: rs12048493	WARNING	No matching proxy snps found

Using version rsnps_0.2.0.9000.

Add support for NCBI eutils API keys

comes via #31

fetch_genotypes

I was trying to download genotype data from opensnp using fetch_genotypes function. But when I looked at internal code, it skips 15 line by default. Actually there are some files where there is not skips at all. For example: https://opensnp.org/data/6.23andme.5

Thanks

bug in ld_search

https://travis-ci.org/ropensci/rsnps#L704

NCBI_snp_query

can we query a large dataset (eg:30,000 SNPids or above)if yes , then please help me how?

Specify assembly build

From user:

They want to specify a specific assembly, e.g. 37. whereas NCBI_snp_query() pulls from the most recent build

Bug in LDSearch

Tracked this down to a bug in NCBI_snp_query()

@kevinushey trying to solve this now, seems that some xml objects contain a <frequency> element, while some do not, and in this line you call the Frequency element from a list, but when it's not there, 😿

Not sure what the appropriate thing to do here is since I'm not familiar with this kind of data?

e.g., here's one that works:

LDSearch(SNPs = 'rs2836443')

But this errors

LDSearch(SNPs = 'rs113196607')

Querying SNAP...
Querying NCBI for up-to-date SNP annotation information...

 Rerun with Debug
 Error in `[<-.data.frame`(`*tmp*`, i, , value = c("rs113196607", "21",  : 
  replacement has 7 items, need 10 

Unexpected warning when calling ld_search

ld_search("rs6004658", dataset = "onekgpilot", panel = "CEU", quiet = FALSE)

yields:

Warning message:
In if (grepl("NCBI", deparse(sys.call()))) { :
  the condition has length > 1 and only the first element will be used

It seems this always happens with ld_search calls that include 3 or more named parameters.

Import all non-base R fxns

see https://cran.rstudio.com/web/checks/check_results_rsnps.html

ld_search returned error

I run the below script in R, and it returns error. Not sure what is wrong.

SNAP<- ld_search("rs11125733", GeneCruiser = FALSE, dataset = "onekgpilot", panel = "CEU", RSquaredLimit = 0.8, distanceLimit = 500)
Querying SNAP...
Querying NCBI for up-to-date SNP annotation information...
Error in stats::setNames(lapply(tmpsplit, parse_data), SNPs) : 
  'names' attribute [75] must be the same length as the vector [73]
In addition: Warning message:
In if (grepl("NCBI", deparse(sys.call()))) { :  the condition has length > 1 and only the first element will be used



R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bindrcpp_0.2                 MendelianRandomization_0.2.0
[3] dplyr_0.7.1                  rsnps_0.2.0                 

dbSNP phasing out non-human data

https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/09/phasing-out-support-for-non-human-genome-organism-data-in-dbsnp-and-dbvar/

does this affect this pkg at all?

donttest examples

This concerns packages using \donttest in their examples. Such code
will be run by example() and hence should be runnable ... yours is
not. With R-devel the \donttest examples can be run by R CMD check
--run-donttest: we have done that and found failures in packages most
of those above, plus ... rsnps

In almost all cases there is something obviously wrong with the
failing example. Please submit an update to CRAN (using the webform, and following the
CRAN policies at http://cran.r-project.org/web/packages/policies.html).
Do NOT reply to this email to submit an update! There may be other issues that need fixing shown on the package's
results page.

select reference build/dbsnp build in ncbi_snp_query2?

It is nice that ncbi_snp_query2 returns metadata on the reference
build used to obtain coordinates. Can parameters be added so that
the query is issued to select earlier builds? I didn't find anything
obvious in the NCBI eutils documentation, but

https://www.ncbi.nlm.nih.gov/variation/view/?q=rs6060535&filters=source:dbsnp&assm=GCF_000001405.33 # is GRCh38

while

https://www.ncbi.nlm.nih.gov/variation/view/?q=rs6060535&filters=source:dbsnp&assm=GCF_000001405.25 # is GRCh37

Thanks

Push new version to CRAN

content changes: encoding and text parse

Maybe set GeneCruiser = FALSE by default?

I have the same issue as #42 , but setting GeneCruiser = FALSE resolves it.

ld_search("rs420358")
Querying SNAP...

Error in split_to_df(tmp, sep = "\t", fixed = TRUE) :
non-equal lengths for each entry of x post-splitting

ld_search("rs420358", GeneCruiser = FALSE)
Querying SNAP...
Querying NCBI for up-to-date SNP annotation information...
Done!

Maybe set GeneCruiser = FALSE by default, as the SNAP is more about LD searching rather than gene mapping?

---

Session:

R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rsnps_0.2.0

loaded via a namespace (and not attached):
 [1] httr_1.2.1    magrittr_1.5  plyr_1.8.4    R6_2.2.0      tools_3.3.2   curl_2.3     
 [7] Rcpp_0.12.10  stringi_1.1.3 stringr_1.2.0 XML_3.98-1.5 

Change fxn name str_split to avoid overlap with stringr::str_split

Hey Kevin, The stringr package has a function named str_split. Would it be possible to change the name of your function to avoid this overlap?

LDSearch should behave more similarly to web's SNAP in regards to query SNPs that are missing in dataset.

LDSearch should behave more similarly to SNAP in regards to query SNPs that are missing in dataset.

Example:

ld_search("rs11571833", dataset = "onekgpilot", panel = "CEU", RSquaredLimit = 0.8,
          distanceLimit = 500, GeneCruiser = FALSE, quiet = FALSE)

outputs

Querying SNAP...
Error: no valid data found
In addition: Warning messages:
1: rs11571833	WARNING	Query snp not in 1000GenomesPilot1 
2: rs11571833	WARNING	No matching proxy snps found 

In my opinion, the first issue is that this behaves differently from the website. SNAP will not break if among the provided list of query SNPs some are missing from the queried dataset.
The second problem is that this breaks the computation of LDSearch when calling it when on a vector of several query SNPs.

Therefore, I think Broad's behavior should be the default behavior of LDSearch. Perhaps the returned list by LDSearch should see the data frames corresponding to the offending query SNPs be removed by assigning to them NULL (in a list this will remove them). In addition, one should add one argument to LDSearch to switch between the old and this new proposed behavior, making the latter the default option.

Plot function for output of ld_search?

It would be nice if ld_search returned a result with "method", so default plot function could be used to plot Position as xaxis vs RSquared value as yaxis.

Example:

x <- ld_search("rs420358")

# instead of this:
plot(x$rs420358$bp_NCBI, x$rs420358$RSquared, xlab = "Position", ylab = bquote("R"^2))

# we could maybe simply:
plot(x, snp = "rs420358")

# or "plot = TRUE" option?
x <- ld_search("rs420358", plot = TRUE)

Remove ropensnp from CRAN

Still at http://cran.r-project.org/web/packages/ropensnp/index.html

Ask maintainers to remove it

Error in ncbi_snp_query2(proxy_SNPs) : Request-URI Too Long (HTTP 414).

I ran the below script in R. It returned error as below.

I think it is because I set a very low RSquaredLimit. Because I want to check all LD information. Is there a way to solve this problem?

SNAP<- ld_search("rs116785524", GeneCruiser = FALSE, dataset = "onekgpilot", panel = "CEU", RSquaredLimit = 0.1, distanceLimit = 500)
Querying SNAP...
Querying NCBI for up-to-date SNP annotation information...
Error in stats::setNames(lapply(tmpsplit, parse_data), SNPs) :  'names' attribute [227] must be the same length as the vector [223]
In addition: Warning message:
In if (grepl("NCBI", deparse(sys.call()))) { : the condition has length > 1 and only the first element will be used

Use beagle data for ld_search?

This package uses beagle RSquared data to get proxies:
https://github.com/slowkow/proxysnps

beagle RSquared data folder, which includes 1KG Phase 3 data:
http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/

Could this be an option for ld_search?

ld_search(SNPs, dataset = "beagle") 

Issue: Curl couldn't connect ncbi_snp_query

Session Info

sessionInfo() 
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so
LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rsnps_0.2.0

loaded via a namespace (and not attached):
 [1] httr_1.3.1     compiler_3.4.2 magrittr_1.5   plyr_1.8.4     R6_2.2.2      
 [6] tools_3.4.2    curl_3.1       Rcpp_0.12.15   stringi_1.1.6  stringr_1.3.0 
[11] XML_3.98-1.10 

Hello,

I'd like to use rsnps to get chromosome position of the SNP however my command fails as:

ncbi_snp_query("rs62635278")
Error in curl::curl_fetch_memory(url, handle = handle) :
Couldn't connect to server

I export proxy settings for my cluster but that doesn't help.

export http_proxy=http:/.....

Tried with https:
export https_proxy=http:/.....

I installed rsnps on local using

R CMD INSTALL rsnp.gz -l ~/R_LIB

Any suggestions?

http://opensnp.org/snps/rs7412.json returns error

allgensnp(snp='rs7412')[1:3]
http://opensnp.org/snps/rs7412.json

returns Error in file(con, "r") : cannot open the connection

It seems that perhaps this method is gone?

Error in LDSearch

I tried an example:
LDSearch('rs113196607')
Querying SNAP...
Error in out$SNP : $ operator is invalid for atomic vectors

Any solutions?

Thanks!

`ld_search` call gives an error: `Error in stats::setNames(lapply(tmpsplit, parse_data), SNPs)`

ld_search("rs10510102", dataset = "onekgpilot", panel = "CEU", RSquaredLimit = 0.4, distanceLimit = 500, GeneCruiser = FALSE, quiet = FALSE)

gives back:

Querying SNAP... Querying NCBI for up-to-date SNP annotation information... Error in stats::setNames(lapply(tmpsplit, parse_data), SNPs) : 'names' attribute [193] must be the same length as the vector [189] In addition: Warning message: In if (grepl("NCBI", deparse(sys.call()))) { : the condition has length > 1 and only the first element will be used

fail well when too many SNPs passed

NCBI correctly gives a 414 Request URI too long error when that is the case, but the function doesn't currently handle this error...

ld_search failing: Broad Institute service down

Anyone know if it's just a short blip in service or if it's down for good?

An example URL sent when calling ld_search

http://archive.broadinstitute.org/mpg/snap/ldsearch.php?snpList=rs113196607&hapMapRelease=onekgpilot&hapMapPanel=CEU&RSquaredLimit=0.8&distanceLimit=500000&downloadType=file&includeQuerySnp=on&submit=search&columnList%5B%5D=DP%2CGA%2CMAF

but then error message is

Server returned HTTP response code: 502 for URL: http://genecruiser.broadinstitute.org/genecruiser3_services/rest/variation/[email protected]&name=rs13052546+rs13051259+rs9976134+rs13052090+rs2836551+rs9977611+rs2212596+rs2244890&firstResult=0

Bug in LDSearch - columnList param not working

this request

http://www.broadinstitute.org/mpg/snap/ldsearch.php?snpList=rs420358&hapMapRelease=onekgpilot&hapMapPanel=CEU&RSquaredLimit=0.8&distanceLimit=500000&downloadType=file&includeQuerySnp=on&submit=search&columnList[]=DP,GA,MAF

fails, and it’s the param columnList that causes failure.

It works if you only use some of the values, e.g., columnList[]=DP

Seems to fail when GA included, e.g., columnList[]=GA

so this query

http://www.broadinstitute.org/mpg/snap/ldsearch.php?snpList=rs420358&hapMapRelease=onekgpilot&hapMapPanel=CEU&RSquaredLimit=0.8&distanceLimit=500000&downloadType=file&includeQuerySnp=on&submit=search&columnList[]=GA

gives

SNP Proxy   Distance    RSquared    GeneVariant GeneName    GeneDescription
Error: null

various problems with ncbi_snps_query...

I am trying to get NCBI’s dbSNP information related to my list of SNPs. I use the R package rsnps and the command ncbi_snp_query and even if i have already checked my list of SNPs that have all rs numbers it gives me this error:

Error: not all items supplied are prefixed with 'rs';
you must supply rs numbers and they should be prefixed with 'rs', e.g. rs420358
In addition: Warning messages:
error: not all items supplied are prefixed with 'rs';you must supply rs numbers and they should be prefixed with 'rs', e.g. rs420358In addition: Warning messages:
1: No chromosomal information for rs9941952; may be unmapped

the second question is why the function stops doing nothing when there is a snp that could be unmapped?

Here my code:

snps<-read.table("snplist.txt") #it has dimension 600k rows and 1 column with the rs-numbers
snps_ok<-as.factor(snps[,])
snp_split<-split(snps_ok, ceiling(seq_along(snps_ok)/200))
snps_info<- lapply(snp_split, ncbi_snp_query)
sapply(snps_info, NROW)

After my lapply command i get the error written above and after the sapply "object snps_info not found". I tried with a subset of 10 snps from my list and it works fine.

I hope someone could help me!
Thanks in advance ;)

Fix example for NCBI_snp_query

from #9

Add examples of using SNPRelate?

Not sure if this makes sense, but seems like combo of getting data through this pkg plus manipulating/analyzing with SNPRelate could be useful to users?

http://cran.r-project.org/web/packages/SNPRelate/index.html

X chromosome delivering NA

Any idea why the following line
NCBI_snp_query(SNPs = "rs6152")
gives me <NA> in the Chromosome column and message thus
Warning message: NAs introduced by coercion

Allow pass on curl options to each fxn

Wrong coordinates

ncbi_snp_query is fetching the wrong coordinates, at least for some ids

library(rsnps)
library(SNPlocs.Hsapiens.dbSNP144.GRCh37)
snps <- SNPlocs.Hsapiens.dbSNP144.GRCh37
ncbi_snp_query('rs378022') # BP = 60464670 WRONG!
snpsById(snps,'rs378022') # 60450403 Correct!

lowercase and snakecase ncbi and ldsearch methods, mark deprecated

NCBI_snp_query: "Assembly" and "Annotation Release" information are missing

It would be awesome to have assembly and annotation release info in the data.frames returned by "NCBI_snp_query"s. Right now, only the chromosome positions are reported, which is somewhat vague when the assembly is not known.

Query	Chromosome	.....	BP	Assembly	Annotation.release
rs9970807	1	.....	56499992	GRCh38	106

and a new argument can be added to NCBI_snp_query function such as "assembly":

NCBI_snp_query('rs9970807', assembly='GRCh38')

Alternatively, there can be multiple columns specifying the position, one column per assembly:

Query	Chromosome	.....	BP.GRCh38	BP.GRCh37.p13
rs9970807	1	.....	56499992	56965664

NCBI_snp_query base-pair position

Hi,

The chromosomal base-pair position given by NCBI_snp_query appears to be off by one base-pair. Is this correct? Or am I missing something?

Thank you,

Luz

use markdown docs

Could you please make it optinal to call `ncbi_snp_query2` in `ld_search`?

Hi Scott, Kevin & Hao,

I am using SNAP to collect negative examples for my regulatory SNP classification research and I really appreciate your work! It saves me a lot of time!

However, I don't understand why you would call ncbi_snp_query2 inside ld_search, because in my situation I hardly use the NCBI columns from the results. Is it possible for you to make this calling an option? Sorry if I missunderstood your design.

Best regards,
Yao

Tests for LDSearch

replace httr with crul

Blarg, opensnp.org is down, putting off progress....

Problem with LDsearch command

The LD search command was working perfectly until yesterday. I am having the following issue now:

Error in split_to_df(tmp, sep = "\t", fixed = TRUE) :
non-equal lengths for each entry of x post-splitting
In addition: Warning message:
In if (grepl("NCBI", deparse(sys.call()))) { :
the condition has length > 1 and only the first element will be used

NCBI_snp_query returns 'position - 1'

Result of NCBI_snp_query('rs9970807')$BP is 56499991, however here it is shown as 56499992. Is this a design decision? If so, I believe it would be better to be consistent with NCBI dbSNP positions.

Some issues with 'NCBI_snp_query' when XML file with 2 components in Assembly Section

When I executed a query by 'NCBI_snp_query', like NCBI_snp_query("rs495135"), found column Gene and BP are with NA value, but indeed there are values in XML file of this SNP# ( Results are expected to be Gene = NOSTRIN, BP = 168830848).
And another example with the same issue, NCBI_snp_query("rs73970001"), but BP value existed in XML file only ( Results are expected to be Gene = N/A, BP = 168896379 ).

I found this issue probably occurred while there are two components in Assembly Section of XML file.

rs495135

<Assembly dbSnpBuild="147" genomeBuild="38.2" groupLabel="GRCh38.p2" current="true" reference="true">
<Component componentType="contig" accession="NW_003315909.1" chromosome="2" gi="303308538" contigLabel="GCF_000001405.28">
<MapLoc asnFrom="486" asnTo="486" locType="exact" alnQuality="1" orient="forward" leftContigNeighborPos="485" rightContigNeighborPos="487" refAllele="G"/>
</Component>
<Component componentType="contig" accession="NT_005403.18" chromosome="2" start="94496015" end="242183528" orientation="fwd" gi="568815346" groupTerm="NC_000002.12" contigLabel="GCF_000001405.28">
<MapLoc asnFrom="74334833" asnTo="74334833" locType="exact" alnQuality="1" orient="forward" physMapInt="168830848" leftContigNeighborPos="74334832" rightContigNeighborPos="74334834" refAllele="G">
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="NM_001039724" mrnaVer="3" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="NM_001171631" mrnaVer="1" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="NM_001171632" mrnaVer="1" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="NM_052946" mrnaVer="3" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="XM_005246270" mrnaVer="1" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="XM_006712233" mrnaVer="2" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="XM_011510540" mrnaVer="1" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="XM_011510541" mrnaVer="1" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="XM_011510542" mrnaVer="1" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="XR_427064" mrnaVer="1" fxnClass="intron-variant" soTerm="intron_variant"/>
<FxnSet geneId="115677" symbol="NOSTRIN" mrnaAcc="XR_922836" mrnaVer="1" fxnClass="intron-variant" soTerm="intron_variant"/>
</MapLoc>
</Component>

rs73970001

<Assembly dbSnpBuild="147" genomeBuild="38.2" groupLabel="GRCh38.p2" current="true" reference="true">
<Component componentType="contig" accession="NW_003315909.1" chromosome="2" gi="303308538" contigLabel="GCF_000001405.28">
<MapLoc asnFrom="83006" asnTo="83006" locType="exact" alnQuality="1" orient="forward" leftContigNeighborPos="83005" rightContigNeighborPos="83007" refAllele="G"/>
</Component>
<Component componentType="contig" accession="NT_005403.18" chromosome="2" start="94496015" end="242183528" orientation="fwd" gi="568815346" groupTerm="NC_000002.12" contigLabel="GCF_000001405.28">
<MapLoc asnFrom="74400364" asnTo="74400364" locType="exact" alnQuality="1" orient="forward" physMapInt="168896379" leftContigNeighborPos="74400363" rightContigNeighborPos="74400365" refAllele="G"/>
</Component>

Is there any solution for this issue ? Thanks u !