Finding SNPs RSID from older papers
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2.6 years ago
ognjen011 ▴ 200

I encountered a paper which test an IL-6 polymorphism, but never clearly specifies it with an RSID, but simply calls it IL-6 -174:

https://www.ncbi.nlm.nih.gov/pubmed/18930842

I tried using online resources to find the exact chromosomal position and thus find the RSID that corresponds to position -174 of IL-6 gene, but I've found no matches at the location I calculated/found. Thus, I would prefer if someone checked my method and help me correct it.

1) What is -174 in reference to? Start of transcription, start of translation? Which position is that for IL-6 gene in GRCh38 or how does one find it exactly? ENSEMBL and Entrez data for the gene beginning differ, which is probably not uncommon.

2) Is there a resource that gives these alternative names so that one can use them as mapping?

3) Is such data likely to change with genome builds? IL-6 is at 7p21 in the paper, but in the current build it is in 7p15, adjacent to 7p21, if I am reading it correctly.

Thanks in advance!

SNP RSID assembly • 573 views
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2.6 years ago
GenoMax 104k

@Denise: Here is a relevant line from intro of the paper

The IL-6 gene, located in humans in the short arm of chromosome 7 (7p21), displays a single nucleotide polymorphism (SNP) in the promoter region (−174 G/C) which seems to be associated to variations of IL-6 gene expression and serum levels (Fishman et al., 1998).

The study referred to by OP is a meta-analysis of 9 studies that were published between 2001-2005.

Here is the polymorphism sequence referred to in Fishman paper:

https://www.ncbi.nlm.nih.gov/nuccore/AF005485

that sequence now UNIQUELY maps here (between the added * in alignment below):

blat-IL6

>chromosome:GRCh38:7:22726595:22727497:1
22726595 TTTGAGGATGGCCAGGCAGTTCTACAACAGCCGCTCACAGGGAGAGCCAGAACACAGAAG 22726654
22726655 AACTCAGATGACTGGTAGTATTACCTTCTTCATAATCCCAGGCTTGGGGGGCTGCGATGG 22726714
22726715 AGTCAGAGGAAACTCAGTTCAGAACATCTTTGGTTTTTACAAATACAAATTAACTGGAAC 22726774
22726775 GCTAAATTCTAGCCTGTTAATCTGGTCACTGAAAAAAAATTTTTTTTTTTTCAAAAAACA 22726834
22726835 TAGCTTTAGCTTATTTTTTTTCTCTTTGTAAAACTTCGTGCATGACTTCAGCTTTACTCT 22726894
22726895 *TTGTCAAGACATGCCAAAGTGCTGAGTCACTAATAAAAGAAAAAAAGAAAGTAAAGGAAG 22726954
22726955 AGTGGTTCTGCTTCTTAGCGCTAGCCTCAATGACGACCTAAGCTGCACTTTTCCCCCTAG 22727014
22727015 TTGTGTCTTGCCATGCTAAAGGACGTCACATTGCACAATCTTAATAAGGTTTCCAATCAG 22727074
22727075 CCCCACCCGCTCTGGCCCCACCCTCACCCTCCAACAAAGATTTATCAAATGTGGGATTTT 22727134
22727135 CCCATGAGTCTCAATATTAGAGTCTCAACCCCCAATAAATATAGGACTGGAGATGTCTGA 22727194
22727195 GGC*TCATTCTGCCCTCGAGCCCACCGGGAACGAAAGAGAAGCTCTATCTCCCCTCCAGGA 22727254
22727255 GCCCAGCTATGAACTCCTTCTCCACAAGTAAGTGCAGGAAATCCTTAGCCCTGGAACTGC 22727314
22727315 CAGCGGCGGTCGAGCCCTGTGTGAGGGAGGGGTGTGTGGCCCAGGGAGGGCTGGCGGGCG 22727374
22727375 GCCAGCAGCAGAGGCAGGCTCCCAGCTGTGCTGTCAGCTCACCCCTGCGCTCGCTCCCCT 22727434
22727435 CCGGCACAGGCGCCTTCGGTCCAGTTGCCTTCTCCCTGGGGCTGCTCCTGGTGTTGCCTG 22727494
22727495 CTG
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Thanks for the reply. Using BLAST is a great idea. Is there a resource that could help me skip BLAST if the sequence has a known accession number? For example, if I know my variant is NM_001105580:c.1394T>C, how would one skip BLAST and directly get the absolute genomic position in the current build?

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NM_001105580:c.1394T>C is a HGVS notation, so I'd expect you could annotate variants like that and find their genomic coordinates plus functional consequences on human transcripts using the VEP. VEP does take HGVS identifiers

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Hey, I've just found the explicit variant: https://www.snpedia.com/index.php/Rs1800795 The position of this base is 22727026. When counting -174 from the end of your aligned sequence, I get a position 22727024. Also, the "real" SNP is C > G. Could you comment on that?

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I see what was done. The accession link is actually: https://www.ncbi.nlm.nih.gov/nuccore/AF039228

And it was sequenced from -550-+61. As a result, -174 is not counted from the end of the sequence as I assumed. Unusual.

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2.6 years ago
Denise CS ★ 5.1k

I can't access the full text as the paper has been published by Elsevier.

But let's have a look at what is available without paying for access. Note the publishing date: Jan 2009. GRCh37 was released in Feb 2009. So the data would have been in NCBI36 at the best; perhaps NCBI35?

Looking for the term longevity in the newly released Open Targets Genetics, selecting one study (Zeng Y 2016, Sci Rep 26912274) out of many others that match that term, then focusing on the signal on chr 7, that leads me to 7_22768027_A_G rs2069837.

Whether or not this is the rsID corresponding to IL-6 -174, I don't know. More exploratory research would be needed. But at least we know the study was not carried out on GRCh37 or GRCh38.

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Thank you for clearly outlying your reasoning.

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