ncbi shows another chromosome of a SNP

Question

[tonja.r]

I have lots of SNPs from GWAS with their positions and chromosomes. According to my data and this page a SNP rs 3000483 is located on chromosome 13. According to NCBI it is on chromosome Y. How can it happen?

Answer 1

[Kamil]

When I take the SNP's flanking sequence from NCBI and align it to hg19 with BLAT I get:

QUERY       SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END
------------------------------------------------------------------------
rs3000483    599     1   600   600 100.0%    13   +   40318925  40319525

Notably, there are no high-scoring positions on chrY for this sequence. The best chrY hit is 3316143, but that is ~450Kb away from the site reported by NCBI at 3763199.

However, UCSC says that the position is chrY 3631240.

I'm not sure where to place this SNP.