Variant report

Variant	rs2959069
Chromosome Location	chr11:4072871-4072872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:4072025-4072881	K562	blood:	n/a	n/a

Variant related genes	Relation type
STIM1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10742229	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030814	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602757	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1442725	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465952	0.87[CEU][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2060822	0.86[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2289570	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412341	0.86[CHB][hapmap]
rs2898950	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920140	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920141	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920142	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923947	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2923951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2923952	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2923954	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959060	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959064	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959071	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959072	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959076	0.85[CHB][hapmap]
rs35695744	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794051	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794052	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910595	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910881	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924858	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926908	0.83[EUR][1000 genomes]
rs7927493	0.90[EUR][1000 genomes]
rs7930739	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938946	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7940635	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7945918	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894455	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9735835	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9988893	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4047800-4077400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:4048000-4077600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:4048600-4077800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:4051000-4080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:4057400-4076800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:4059200-4076800	Weak transcription	GM12878-XiMat	blood
7	chr11:4062000-4080400	Weak transcription	Spleen	Spleen
8	chr11:4062200-4076600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr11:4062800-4076200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr11:4063600-4076400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:4066000-4079200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:4066200-4076600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:4066200-4078400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:4066200-4079000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr11:4066200-4079200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:4066200-4104200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:4066400-4076800	Weak transcription	Fetal Stomach	stomach
18	chr11:4066400-4077400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr11:4066400-4077400	Weak transcription	Esophagus	oesophagus
20	chr11:4066400-4077600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:4066400-4107800	Weak transcription	Small Intestine	intestine
22	chr11:4066600-4075600	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:4066600-4075800	Weak transcription	Primary B cells from cord blood	blood
24	chr11:4066600-4076600	Weak transcription	Adipose Nuclei	Adipose
25	chr11:4066600-4076800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:4066600-4076800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:4066600-4077600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:4066600-4077600	Weak transcription	Left Ventricle	heart
29	chr11:4066600-4078400	Weak transcription	NHDF-Ad	bronchial
30	chr11:4066600-4078600	Weak transcription	K562	blood
31	chr11:4066600-4078600	Weak transcription	Osteobl	bone
32	chr11:4066600-4080200	Weak transcription	Right Ventricle	heart
33	chr11:4066600-4080400	Weak transcription	Fetal Lung	lung
34	chr11:4066600-4080400	Weak transcription	Gastric	stomach
35	chr11:4066600-4085800	Weak transcription	Pancreas	Pancrea
36	chr11:4066800-4076800	Weak transcription	Liver	Liver
37	chr11:4066800-4078400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:4067000-4076800	Weak transcription	Brain Anterior Caudate	brain
39	chr11:4067000-4079200	Weak transcription	Colon Smooth Muscle	Colon
40	chr11:4067000-4087400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:4067800-4076800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:4067800-4079200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr11:4067800-4080400	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:4067800-4080600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:4067800-4093200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:4068000-4076800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:4068000-4077600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:4068000-4079000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:4068000-4079200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:4068000-4079400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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