Variant report

Variant	rs6425438
Chromosome Location	chr1:171791211-171791212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171785613..171787627-chr1:171789053..171791436,2	K562	blood:
2	chr1:171788325..171792054-chr1:171792215..171794948,3	MCF-7	breast:
3	chr1:171787129..171789980-chr1:171790659..171793277,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224600	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10436867	0.92[CEU][hapmap]
rs10798636	0.85[GIH][hapmap]
rs10798667	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798692	0.80[CHD][hapmap];0.81[MEX][hapmap]
rs10913644	0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11579330	0.92[CEU][hapmap]
rs11587288	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs12025368	0.92[CEU][hapmap]
rs12032340	0.85[MEX][hapmap]
rs12034454	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs12566700	0.81[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs16843385	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2232812	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs2232816	0.87[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs2232818	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs2232826	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs2294717	0.87[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2294723	0.81[MEX][hapmap]
rs3753538	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs56178029	0.90[ASN][1000 genomes]
rs57476157	0.87[ASN][1000 genomes]
rs59302445	0.95[ASN][1000 genomes]
rs60502293	0.92[ASN][1000 genomes]
rs6425423	0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6425439	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6684594	0.94[ASN][1000 genomes]
rs6691222	0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6695502	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs72703115	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711798	0.84[EUR][1000 genomes]
rs7518914	0.81[CHB][hapmap]
rs7538839	0.92[CEU][hapmap]
rs7541192	0.87[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs7543608	0.91[ASN][1000 genomes]
rs7548462	0.94[ASN][1000 genomes]
rs7860	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs909958	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6425438	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs6425438	SELL	cis	cerebellum	SCAN
rs6425438	DNM3	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171770200-171794600	Weak transcription	Primary T cells from cord blood	blood
2	chr1:171773000-171796000	Weak transcription	Pancreas	Pancrea
3	chr1:171787600-171795800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:171787600-171796000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:171787800-171792600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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