Variant report

Variant	rs1938929
Chromosome Location	chr11:86334064-86334065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86333716..86335655-chr11:86521325..86523278,2	MCF-7	breast:
2	chr11:86332972..86336293-chr11:86338009..86340844,3	MCF-7	breast:
3	chr11:86332528..86334846-chr11:86511454..86513733,3	MCF-7	breast:
4	chr11:86332654..86334569-chr11:86510961..86513422,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10792865	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11234719	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234731	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12274942	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12282010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs12288119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1938921	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1938931	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938932	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938935	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017483	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2212340	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2212341	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4144866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245417	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245418	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245419	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245420	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245421	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245422	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245423	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245424	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319536	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4439535	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4592448	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4943948	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4943949	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944602	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944603	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944607	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944609	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944618	0.85[ASN][1000 genomes]
rs496167	0.90[ASN][1000 genomes]
rs538058	0.82[CHB][hapmap]
rs550168	0.81[ASN][1000 genomes]
rs647782	0.87[ASN][1000 genomes]
rs656307	0.90[ASN][1000 genomes]
rs6592301	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661954	0.81[CHB][hapmap]
rs663543	0.90[ASN][1000 genomes]
rs679220	0.82[CHB][hapmap]
rs7105863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106865	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[ASN][1000 genomes]
rs7115580	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123044	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7937853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948981	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7951868	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv898057	chr11:86306401-86335459	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86321800-86343200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:86322000-86334200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:86322000-86334200	Weak transcription	Left Ventricle	heart
4	chr11:86330800-86341600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:86331000-86343600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:86331000-86346200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr11:86332000-86334200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:86332000-86335600	Enhancers	Fetal Heart	heart
9	chr11:86332200-86334200	Weak transcription	Brain Anterior Caudate	brain
10	chr11:86332200-86334200	Weak transcription	Psoas Muscle	Psoas
11	chr11:86332200-86334200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:86332200-86338800	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:86332400-86335000	Weak transcription	NHLF	lung
14	chr11:86332400-86337000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr11:86332800-86336000	Enhancers	Right Atrium	heart
16	chr11:86332800-86343200	Weak transcription	A549	lung
17	chr11:86333000-86334200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:86333000-86335000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:86333000-86342400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr11:86333200-86334200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:86333200-86334200	Weak transcription	Osteobl	bone
22	chr11:86333200-86334600	Enhancers	HMEC	breast
23	chr11:86333200-86335800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:86333200-86335800	Weak transcription	Adipose Nuclei	Adipose
25	chr11:86333200-86336200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:86333200-86336400	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:86333200-86338000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:86333200-86338600	Weak transcription	Fetal Lung	lung
29	chr11:86333200-86338800	Weak transcription	HSMMtube	muscle
30	chr11:86333200-86339000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr11:86333200-86349800	Weak transcription	Esophagus	oesophagus
32	chr11:86333400-86334200	Weak transcription	Pancreas	Pancrea
33	chr11:86333400-86335000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:86333400-86336600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:86333600-86334400	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr11:86333600-86335200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:86333800-86334200	Weak transcription	NHDF-Ad	bronchial
38	chr11:86333800-86334800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr11:86333800-86334800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:86334000-86334200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:86334000-86334400	Flanking Active TSS	NHEK	skin
42	chr11:86334000-86334800	Enhancers	Rectal Smooth Muscle	rectum
43	chr11:86334000-86335000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr11:86334000-86335000	Enhancers	NH-A	brain
45	chr11:86334000-86335200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:86334000-86338800	Weak transcription	Right Ventricle	heart
47	chr11:86334000-86342200	Enhancers	Ovary	ovary

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