Variant report

Variant	rs3824956
Chromosome Location	chr11:85370482-85370483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85369773..85371949-chr3:161088766..161091277,2	MCF-7	breast:
2	chr11:85368615..85371955-chr11:85778453..85780555,3	MCF-7	breast:
3	chr11:85369899..85372804-chr11:85545062..85546579,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1046216	0.94[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11600919	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11603256	0.88[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11606688	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11821005	0.85[ASN][1000 genomes]
rs1237203	0.89[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs1354397	0.81[CHB][hapmap]
rs17148293	0.91[AFR][1000 genomes]
rs2117312	0.89[ASN][1000 genomes]
rs2196168	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290823	0.94[ASW][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs290173	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs290174	0.81[ASN][1000 genomes]
rs290179	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs290180	0.86[CHB][hapmap];0.92[CHD][hapmap];0.88[ASN][1000 genomes]
rs290181	0.89[ASN][1000 genomes]
rs290183	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs290184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290185	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs290190	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs290195	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs290200	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs290202	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs35844123	0.87[AFR][1000 genomes]
rs370385	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs3753050	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781815	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3817087	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3862782	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4301809	0.83[ASN][1000 genomes]
rs431606	0.86[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs491867	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4944526	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4944530	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496187	0.81[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs522604	0.91[ASN][1000 genomes]
rs540063	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs550404	0.90[JPT][hapmap]
rs552013	0.95[ASN][1000 genomes]
rs556669	0.90[JPT][hapmap]
rs57296431	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs575050	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs57549298	0.89[ASN][1000 genomes]
rs580459	0.90[JPT][hapmap]
rs589327	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs592460	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs597480	0.90[JPT][hapmap]
rs61114547	0.87[ASN][1000 genomes]
rs61567739	0.81[ASN][1000 genomes]
rs631410	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs641393	0.90[JPT][hapmap]
rs647912	0.81[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs679204	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs680498	0.81[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs7107788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7113528	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7116195	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7119617	0.94[ASW][hapmap];0.86[LWK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs7122887	0.85[ASN][1000 genomes]
rs7925739	0.91[ASN][1000 genomes]
rs7940714	0.82[ASN][1000 genomes]
rs7943586	0.94[ASW][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs7948778	0.86[YRI][hapmap]
rs881120	0.83[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.96[YRI][hapmap];0.95[ASN][1000 genomes]
rs956202	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv898047	chr11:85180409-85377707	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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
6	nsv898048	chr11:85206156-85404138	Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85359400-85373000	Weak transcription	Small Intestine	intestine
2	chr11:85359400-85374000	Weak transcription	Esophagus	oesophagus
3	chr11:85359600-85373000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:85359600-85373400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:85359800-85372600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:85359800-85373000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:85359800-85373000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:85359800-85373000	Weak transcription	Ovary	ovary
9	chr11:85359800-85373200	Weak transcription	Fetal Stomach	stomach
10	chr11:85360000-85373000	Weak transcription	Colonic Mucosa	Colon
11	chr11:85360200-85371200	Weak transcription	Fetal Brain Male	brain
12	chr11:85360200-85372200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:85360200-85373000	Weak transcription	Thymus	Thymus
14	chr11:85360400-85373000	Weak transcription	Right Ventricle	heart
15	chr11:85360400-85373200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:85360400-85374000	Weak transcription	Lung	lung
17	chr11:85360400-85374000	Weak transcription	Pancreas	Pancrea
18	chr11:85360400-85374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:85360600-85371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr11:85360800-85372600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:85360800-85372600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:85361400-85373000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:85362400-85372600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr11:85362600-85374200	Weak transcription	Spleen	Spleen
25	chr11:85362800-85371000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:85362800-85371000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:85362800-85372000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:85362800-85373400	Weak transcription	Left Ventricle	heart
29	chr11:85363000-85373000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr11:85363200-85373000	Weak transcription	Aorta	Aorta
31	chr11:85363200-85373000	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:85363800-85371000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:85364000-85373000	Strong transcription	Placenta	Placenta
34	chr11:85364200-85371000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:85364400-85372600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr11:85364600-85371200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:85364600-85371800	Strong transcription	Fetal Thymus	thymus
38	chr11:85364600-85372000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr11:85364600-85372000	Weak transcription	Fetal Kidney	kidney
40	chr11:85364600-85372200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr11:85364800-85371000	Weak transcription	HepG2	liver
42	chr11:85365400-85372600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr11:85365600-85371000	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:85365600-85371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:85365600-85371400	Weak transcription	Fetal Brain Female	brain
46	chr11:85365600-85373000	Weak transcription	Psoas Muscle	Psoas
47	chr11:85365800-85373000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:85366000-85371600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:85366000-85373000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr11:85366200-85370600	Strong transcription	Liver	Liver

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