Variant report

Variant	rs6596866
Chromosome Location	chr6:1995508-1995509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1993624..1996051-chr6:2001806..2003962,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1004779	0.89[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs10458057	0.84[ASN][1000 genomes]
rs11242729	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs11242732	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs11242733	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12198576	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12201717	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12206316	0.84[ASN][1000 genomes]
rs12212194	0.81[ASN][1000 genomes]
rs2026446	0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs2325727	0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2325758	0.84[ASN][1000 genomes]
rs2325759	0.89[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2325760	0.84[ASN][1000 genomes]
rs4367413	0.94[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs4412249	0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs4427041	0.87[ASN][1000 genomes]
rs4529335	0.85[ASN][1000 genomes]
rs476594	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs495550	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs4959621	0.89[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4959622	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4959624	0.85[ASN][1000 genomes]
rs4959625	0.85[ASN][1000 genomes]
rs4959626	0.85[ASN][1000 genomes]
rs4959627	0.85[ASN][1000 genomes]
rs4959630	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs522175	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs524186	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs610570	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs612278	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs62390707	0.84[ASN][1000 genomes]
rs624545	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs6596867	0.89[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6596870	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs667256	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs676015	0.92[JPT][hapmap]
rs6899584	0.85[ASN][1000 genomes]
rs6900744	0.86[ASN][1000 genomes]
rs6900931	0.86[ASN][1000 genomes]
rs6906509	0.85[ASN][1000 genomes]
rs6908469	0.87[ASN][1000 genomes]
rs6913715	0.85[ASN][1000 genomes]
rs6918847	0.85[ASN][1000 genomes]
rs6924458	0.83[ASN][1000 genomes]
rs6925298	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs6925459	0.85[ASN][1000 genomes]
rs72830106	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72830121	0.83[ASN][1000 genomes]
rs7751074	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs7757144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7761643	0.85[ASN][1000 genomes]
rs9328079	0.84[ASN][1000 genomes]
rs9378321	0.95[CHB][hapmap];0.92[JPT][hapmap]
rs9378323	0.83[CHB][hapmap]
rs9501788	0.87[ASN][1000 genomes]
rs9501789	0.85[ASN][1000 genomes]
rs9503063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503066	0.87[ASN][1000 genomes]
rs9503069	0.85[ASN][1000 genomes]
rs9503077	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2763525	chr6:1994892-2006033	Enhancers Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6596866	FOXQ1	cis	parietal	SCAN
rs6596866	NQO2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1985000-2010200	Weak transcription	Fetal Intestine Large	intestine
2	chr6:1987400-2003600	Weak transcription	Aorta	Aorta
3	chr6:1988400-2008600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:1990200-2008600	Weak transcription	Pancreas	Pancrea
5	chr6:1990400-2010800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:1992800-1997800	Weak transcription	Gastric	stomach
7	chr6:1992800-2010200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:1993000-2021200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:1993200-2005400	Weak transcription	HepG2	liver
10	chr6:1993200-2007200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:1993400-2000400	Weak transcription	Primary T cells from cord blood	blood
12	chr6:1993800-2001000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:1994400-1995800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:1995000-1996200	Weak transcription	GM12878-XiMat	blood
15	chr6:1995400-1996200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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