Hi anyone help me getting BRCA1 & 2 SNP data of Indian population. Any specific database other than dbSNP and BIC?
Thanks every one
You might consider 1000genomes.
I'm using coordinates from GRCh37.p13:
tabix $f 17:41196312-41277500 | gzip > BRCA1.vcf.gz
zcat BRCA1.vcf.gz | wc -l
tabix $f 13:32889617-32973809 | gzip > BRCA2.vcf.gz
zcat BRCA2.vcf.gz | wc -l
I would recommend using the Indian Genome Variation Browser
You have the ability to search for a gene/region e.g incase of BRCA1. Once there you can select the SNPs from their phase1/2 data and get the frequency distribution amongst different Indian populations e.g for rs8176265
I'd also add ExAC which has a much larger cohort than 1000 Genomes and includes allele frequencies for south asian populations. You cannot sub divide that into Indians though.
There was ReliBRCA database but it seems that it does not exist anymore!
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