Day-09 - OMIM

Post date: Jul 11, 2011 4:10:05 PM

Can we identify any SNPs, predicted to be damaging, in OMIM? This would point to any Mendelian traits/disorders I might have. There is a file in dbSNP that is useful for this - The file links omim ids to SNP ids.



gunzip OmimVarLocusIdSNP.bcp.gz

cut -f 1,9 OmimVarLocusIdSNP.bcp | gawk '{print "rs"$2,$1 }' | sort > snps_2_omim.txt

Then, sort my missense SNPs and join both lists. None of my rare missense match, so I checked the larger list of all 476 missense SNPs:

join all_missense.sorted.txt snps_2_omim.txt

You can then just look up the OMIM entries listed, e.g.

rs10246939 607751 <-- This polymorphism, in conjunction with other SNPs in the gene, give rise to the ability to taste or not taste phenylthiocarbamide

rs1049550 612388 <-- strongly associated with sarcoidosis


rs1126809 601800 <-- association with skin sensitivity to sun (p = 7.1 x 10(-13)) and blue versus green eye color (p = 4.6 x 10(-21)).

rs1126809 606933 <-- blue eye colour

rs1154510 609695 <-- HAWKINSINURIA (autosomal dominant inborn error of metabolism) (elevated levels of blood tyrosine and massive excretion of tyrosine derivatives into urine)

rs2108622 122700 <-- resistance to warfarin

rs2108622 604426 <-- resistance to warfarin

rs288326 605083 <-- OSTEOARTHRITIS SUSCEPTIBILITY 1 (strong risk factor for primary osteoarthritis of the hip in females)

rs3775291 603029 <-- protective against the development of geographic atrophy or advanced dry age-related macular degeneration

rs3775291 603075 <-- associated with protection from progression to geographic atrophy in patients with age-related macular degeneration

rs4673 608508 <-- cardiovascular disease related

rs4917 138680 <-- an increased risk for leanness (OR, 1.90; p = 0.027)

rs602662 182100 <-- ...genetic factors affecting circulating vitamin B12 levels and identified rs602662 in the FUT2 gene

rs602662 612542 <-- vit B12


rs7080536 603924 <-- CAROTID STENOSIS, SUSCEPTIBILITY TO (basically a heart disease risk factor)

rs7133914 609007 <-- Decreased susceptibility to Parkinson Disease

rs7308720 609007 <-- Decreased susceptibility to Parkinson Disease

So, overall I think some interesting stuff in there, although alot of this is covered nicely by 23&me already.