Variant report

Variant	rs11889527
Chromosome Location	chr2:54226315-54226316
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	chr2:54196569..54199528-chr2:54223606..54226357,2	MCF-7	breast:
2	chr2:54223813..54226322-chr2:54234091..54236804,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1001296	1.00[CHB][hapmap]
rs10180492	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10181332	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10188834	0.83[AMR][1000 genomes]
rs10190353	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10199041	1.00[CHB][hapmap]
rs10199995	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10207892	1.00[CHB][hapmap]
rs10208649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10496027	0.86[YRI][hapmap]
rs1049894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs11125517	0.83[AMR][1000 genomes]
rs11125521	1.00[CHB][hapmap]
rs11884327	1.00[CHB][hapmap]
rs11884857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11886366	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887593	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11890472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11891000	0.82[EUR][1000 genomes]
rs11891079	1.00[CHB][hapmap]
rs11896279	1.00[CHB][hapmap]
rs11904365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13390377	1.00[CHB][hapmap]
rs13395751	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401491	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13401719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13414565	1.00[CHB][hapmap]
rs13417051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs13425337	1.00[CHB][hapmap]
rs13432387	0.88[AMR][1000 genomes]
rs17039541	0.95[YRI][hapmap]
rs17045242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17045513	1.00[CHB][hapmap]
rs17045575	1.00[CHB][hapmap]
rs17189680	1.00[CHB][hapmap]
rs1872328	1.00[CHB][hapmap]
rs2090182	1.00[CHB][hapmap]
rs2112120	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2161083	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2287347	0.80[CEU][hapmap]
rs28571698	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28699646	0.88[AMR][1000 genomes]
rs3930909	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs41536750	0.88[AMR][1000 genomes]
rs4553857	1.00[CHB][hapmap]
rs58920915	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60769690	0.83[AMR][1000 genomes]
rs60776154	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6545367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545368	0.80[CEU][hapmap]
rs6545369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545382	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6715161	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719990	1.00[AMR][1000 genomes]
rs6723722	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6730494	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6745729	0.88[AMR][1000 genomes]
rs6748686	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6751340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6756424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6761648	0.82[EUR][1000 genomes]
rs72904915	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906704	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906711	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906714	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7556936	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7559651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7567556	1.00[CHB][hapmap]
rs7567614	1.00[CHB][hapmap]
rs7583508	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7588134	0.87[AMR][1000 genomes]
rs7588319	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7594400	1.00[CHB][hapmap]
rs7604464	1.00[CHB][hapmap]
rs7608085	0.88[AMR][1000 genomes]
rs9678301	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
2	chr2:54204400-54226400	Weak transcription	Pancreas	Pancrea
3	chr2:54206000-54226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:54208400-54248200	Weak transcription	Lung	lung
5	chr2:54211400-54243000	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
7	chr2:54215000-54242800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:54216400-54242000	Weak transcription	Fetal Intestine Small	intestine
9	chr2:54216600-54226400	Weak transcription	Ovary	ovary
10	chr2:54217000-54236600	Weak transcription	Brain Angular Gyrus	brain
11	chr2:54217000-54236800	Weak transcription	Brain Anterior Caudate	brain
12	chr2:54217000-54248200	Weak transcription	Gastric	stomach
13	chr2:54217200-54233800	Weak transcription	HepG2	liver
14	chr2:54217200-54239600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:54219200-54226800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:54222400-54227000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:54222400-54228400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr2:54222600-54227000	Enhancers	Primary T cells from cord blood	blood
19	chr2:54224400-54239600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:54225200-54226800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:54225200-54226800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:54225200-54228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:54225600-54227000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr2:54225600-54228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:54225800-54226600	Enhancers	Primary B cells from peripheral blood	blood
26	chr2:54225800-54226600	Enhancers	Brain Germinal Matrix	brain
27	chr2:54225800-54226600	Enhancers	Psoas Muscle	Psoas
28	chr2:54225800-54226800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr2:54225800-54226800	Enhancers	Primary hematopoietic stem cells	blood
30	chr2:54225800-54226800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:54225800-54226800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:54225800-54226800	Enhancers	Colon Smooth Muscle	Colon
33	chr2:54226000-54226600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:54226000-54226600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr2:54226000-54226600	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr2:54226000-54226600	Enhancers	Stomach Smooth Muscle	stomach
37	chr2:54226000-54231000	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:54226000-54240000	Weak transcription	Primary B cells from cord blood	blood
39	chr2:54226200-54226600	Enhancers	Thymus	Thymus
40	chr2:54226200-54226800	Enhancers	Right Atrium	heart
41	chr2:54226200-54239600	Weak transcription	Adipose Nuclei	Adipose

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