Variant report

Variant	rs2460699
Chromosome Location	chr6:71588806-71588807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2038477	0.82[CEU][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs2460692	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2474914	0.84[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2474915	0.85[CEU][hapmap];0.81[CHB][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2474916	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504747	0.81[EUR][1000 genomes]
rs2504748	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2504749	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2504750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2504751	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2504752	0.84[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2504753	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3734371	0.81[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3734372	0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs483894	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs576516	1.00[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs746121	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2460699	BAI3	cis	cerebellum	SCAN
rs2460699	B3GAT2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71584400-71595800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:71584800-71594200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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