Variant report

Variant	rs12421199
Chromosome Location	chr11:36235473-36235474
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:36235314..36237766-chr11:36240242..36242085,2	MCF-7	breast:

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1001715	1.00[LWK][hapmap]
rs11033442	1.00[LWK][hapmap]
rs11033500	1.00[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs11033501	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11033503	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11033504	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11033508	0.81[EUR][1000 genomes]
rs11551023	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11600365	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11601619	0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11602141	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11602754	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11603025	0.86[EUR][1000 genomes]
rs11603810	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11604341	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11604381	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11604397	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11604998	1.00[GIH][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs11605921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11605927	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11605931	0.97[EUR][1000 genomes]
rs11605941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11606074	0.82[CEU][hapmap];0.92[AMR][1000 genomes]
rs11606476	0.84[EUR][1000 genomes]
rs11606598	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11607231	0.86[EUR][1000 genomes]
rs12420852	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12421151	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12421400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12574172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12574173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12574419	1.00[CEU][hapmap];0.80[CHD][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12574525	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12575304	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12575540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12575617	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12575645	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12576603	1.00[LWK][hapmap]
rs12577437	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1374376	0.85[CHB][hapmap];0.89[CHD][hapmap]
rs1405095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1526058	0.86[EUR][1000 genomes]
rs1526059	0.86[EUR][1000 genomes]
rs16928506	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16928509	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16928510	0.84[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16928513	0.89[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16928514	0.89[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16928552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2289980	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2289981	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34213469	0.86[EUR][1000 genomes]
rs34892666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3812769	0.89[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3812771	0.89[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3812772	0.89[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3980393	0.85[CHB][hapmap]
rs4417242	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4417243	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4468324	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4485080	1.00[CEU][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs4611176	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58048041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58356552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58648806	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58707777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59051429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59137935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59307065	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60008257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60544801	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60759289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60823142	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61254236	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61879011	0.92[AMR][1000 genomes]
rs61879013	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs61879034	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61879035	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61879036	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61879037	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61879038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61879039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61879040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61879041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61879261	0.86[EUR][1000 genomes]
rs61879262	0.86[EUR][1000 genomes]
rs61879263	0.83[EUR][1000 genomes]
rs61879264	0.86[EUR][1000 genomes]
rs61879265	0.86[EUR][1000 genomes]
rs61879266	0.86[EUR][1000 genomes]
rs61879267	0.86[EUR][1000 genomes]
rs61879268	0.86[EUR][1000 genomes]
rs61879269	0.86[EUR][1000 genomes]
rs61879270	0.86[EUR][1000 genomes]
rs61879271	0.86[EUR][1000 genomes]
rs61879272	0.86[EUR][1000 genomes]
rs61879273	0.86[EUR][1000 genomes]
rs61879274	0.86[EUR][1000 genomes]
rs61879275	0.86[EUR][1000 genomes]
rs61879277	0.84[EUR][1000 genomes]
rs61879278	0.84[EUR][1000 genomes]
rs61881463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61881464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61881465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61881468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61881469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61881470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61881476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61881477	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61881478	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61881481	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61881484	0.86[EUR][1000 genomes]
rs61881485	0.86[EUR][1000 genomes]
rs61881486	0.86[EUR][1000 genomes]
rs61881487	0.86[EUR][1000 genomes]
rs7110064	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72937449	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72937454	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72937494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72941791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs872534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs921085	0.86[EUR][1000 genomes]
rs940923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv897225	chr11:36136912-36244190	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36218000-36252200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:36219200-36248600	Weak transcription	Ovary	ovary
3	chr11:36220600-36241600	Weak transcription	HSMM	muscle
4	chr11:36221400-36248800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr11:36222000-36239800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:36222800-36248800	Weak transcription	HSMMtube	muscle
7	chr11:36226800-36241600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:36227000-36238400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:36229400-36236600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:36231400-36237800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr11:36231600-36237200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:36232200-36241400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:36232800-36235800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:36232800-36235800	Enhancers	Fetal Lung	lung
15	chr11:36232800-36237200	Enhancers	Brain Hippocampus Middle	brain
16	chr11:36232800-36237800	Enhancers	Brain Substantia Nigra	brain
17	chr11:36233000-36235800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:36233000-36236000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:36233000-36236200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:36233000-36237200	Enhancers	Fetal Brain Male	brain
21	chr11:36233000-36237600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr11:36233200-36237600	Enhancers	Brain Anterior Caudate	brain
23	chr11:36233400-36237800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:36233800-36237800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr11:36234000-36244600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:36234200-36235800	Weak transcription	Fetal Intestine Large	intestine
27	chr11:36234600-36236400	Weak transcription	Fetal Kidney	kidney
28	chr11:36234800-36241000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:36234800-36248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:36234800-36254000	Weak transcription	Right Atrium	heart
31	chr11:36235000-36235600	Bivalent Enhancer	Fetal Stomach	stomach
32	chr11:36235000-36237000	Enhancers	Esophagus	oesophagus
33	chr11:36235000-36237200	Enhancers	NHEK	skin
34	chr11:36235000-36237800	Enhancers	Brain Cingulate Gyrus	brain
35	chr11:36235200-36236200	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:36235200-36236800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:36235200-36237000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:36235200-36237000	Enhancers	HMEC	breast
39	chr11:36235200-36237600	Enhancers	Brain Germinal Matrix	brain
40	chr11:36235200-36238800	Enhancers	Fetal Intestine Small	intestine
41	chr11:36235400-36237400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:36235400-36237600	Enhancers	Fetal Brain Female	brain

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