Variant report

Variant	rs1107312
Chromosome Location	chr3:50539219-50539220
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	chr3:50536244..50539844-chr3:50540439..50543863,5	MCF-7	breast:
2	chr3:50531296..50533562-chr3:50538381..50540201,2	K562	blood:

Variant related genes	Relation type
ENSG00000007402	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1034408	1.00[CEU][hapmap]
rs1034409	1.00[CEU][hapmap]
rs1077215	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs11130253	1.00[TSI][hapmap]
rs12486143	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12487817	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489607	0.85[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs12491440	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs12491812	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494094	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12494326	0.88[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs12494707	0.88[AMR][1000 genomes]
rs17050991	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17050995	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17051000	0.84[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17051025	1.00[TSI][hapmap]
rs17051043	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs17051045	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs1894459	0.84[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2035484	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs2157328	1.00[CEU][hapmap]
rs2170840	0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs2187815	1.00[CEU][hapmap]
rs2227292	0.85[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2227293	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2236969	1.00[CEU][hapmap]
rs2236972	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2236977	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2236978	1.00[CEU][hapmap]
rs2236982	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2236990	1.00[CEU][hapmap]
rs2239750	0.80[ASN][1000 genomes]
rs2239751	0.84[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs2239752	0.85[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs2239753	0.80[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs2282757	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2285090	0.85[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3749265	0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs3752449	0.80[ASN][1000 genomes]
rs3792323	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs3806706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4422301	1.00[CEU][hapmap]
rs4640555	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4688705	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs4688707	0.80[ASN][1000 genomes]
rs4688709	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4688710	0.80[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4688713	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4688715	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4688716	0.88[ASN][1000 genomes]
rs56170012	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60552073	0.83[AMR][1000 genomes]
rs61193866	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61316441	0.80[ASN][1000 genomes]
rs61574029	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61613532	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs616689	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs6446203	1.00[CEU][hapmap]
rs6766638	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6767505	1.00[CEU][hapmap]
rs6770258	1.00[CEU][hapmap]
rs6770669	1.00[CEU][hapmap]
rs6771348	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs728902	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs72938758	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73835531	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs743753	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs743754	1.00[CEU][hapmap]
rs743755	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs743859	1.00[CEU][hapmap]
rs745356	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7610830	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7626470	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs762889	0.85[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7634307	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7642779	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7647409	1.00[CEU][hapmap]
rs7649603	1.00[CEU][hapmap]
rs808148	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs876103	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs876104	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs876105	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs9814874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9817768	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs9828829	1.00[CEU][hapmap]
rs9837658	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs9854585	1.00[CEU][hapmap]
rs9863307	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs9879397	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs9883635	1.00[CEU][hapmap]
rs9990256	1.00[CEU][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50529000-50539600	Weak transcription	Right Atrium	heart
2	chr3:50529800-50539400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:50529800-50540000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:50534000-50539400	Weak transcription	Gastric	stomach
5	chr3:50537000-50539600	Weak transcription	Pancreas	Pancrea
6	chr3:50538000-50539400	Weak transcription	Lung	lung
7	chr3:50538000-50539600	Weak transcription	Spleen	Spleen
8	chr3:50538200-50539400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:50538600-50540000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:50538800-50539600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:50538800-50539800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:50538800-50539800	Weak transcription	Right Ventricle	heart
13	chr3:50539000-50541400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:50539200-50539400	Bivalent Enhancer	Brain Germinal Matrix	brain
15	chr3:50539200-50539400	Bivalent Enhancer	Fetal Heart	heart
16	chr3:50539200-50539600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr3:50539200-50539600	Bivalent/Poised TSS	Fetal Brain Female	brain
18	chr3:50539200-50539600	Bivalent Enhancer	Fetal Kidney	kidney
19	chr3:50539200-50539800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:50539200-50539800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr3:50539200-50539800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr3:50539200-50539800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:50539200-50539800	Bivalent Enhancer	Fetal Intestine Large	intestine
24	chr3:50539200-50540800	Bivalent Enhancer	Fetal Brain Male	brain

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