Variant report

Variant	rs2959071
Chromosome Location	chr11:4066656-4066657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10742229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602757	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1442725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465952	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1662163	0.87[CEU][hapmap]
rs1735053	0.87[CEU][hapmap]
rs2060822	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2289570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412341	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs2898950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920137	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920140	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923947	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2923951	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2923952	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2923954	0.91[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	0.88[CEU][hapmap];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]
rs2959069	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959073	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959076	0.85[CHB][hapmap]
rs35695744	1.00[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	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910874	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910881	1.00[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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7940635	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7945918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894457	0.87[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:82 , 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	chr11:4049600-4070600	Weak transcription	Thymus	Thymus
5	chr11:4050200-4070800	Weak transcription	Fetal Thymus	thymus
6	chr11:4051000-4080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:4051200-4070200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr11:4057400-4076800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:4058200-4070800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:4058800-4070800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:4059200-4076800	Weak transcription	GM12878-XiMat	blood
12	chr11:4062000-4080400	Weak transcription	Spleen	Spleen
13	chr11:4062200-4068200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr11:4062200-4070000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:4062200-4070400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:4062200-4070800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:4062200-4076600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr11:4062600-4067400	Weak transcription	Primary T cells from cord blood	blood
19	chr11:4062600-4070800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr11:4062800-4076200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:4063000-4068800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:4063200-4070800	Weak transcription	Aorta	Aorta
23	chr11:4063600-4076400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:4064600-4068200	Enhancers	HepG2	liver
25	chr11:4064800-4070600	Weak transcription	Dnd41	blood
26	chr11:4065000-4066800	Enhancers	Liver	Liver
27	chr11:4065000-4067800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:4065200-4066800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:4065200-4066800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:4065200-4067000	Enhancers	Colon Smooth Muscle	Colon
31	chr11:4065200-4067200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:4065200-4068000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr11:4065200-4068000	Enhancers	Brain Cingulate Gyrus	brain
34	chr11:4065200-4068200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:4065200-4068200	Enhancers	NHEK	skin
36	chr11:4065400-4066800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:4065400-4066800	Enhancers	Brain Hippocampus Middle	brain
38	chr11:4065400-4066800	Enhancers	Placenta Amnion	Placenta Amnion
39	chr11:4065400-4067000	Enhancers	Brain Angular Gyrus	brain
40	chr11:4065400-4067000	Enhancers	Brain Anterior Caudate	brain
41	chr11:4065400-4068000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:4065400-4068000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:4065400-4068000	Enhancers	Rectal Smooth Muscle	rectum
44	chr11:4065800-4067000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:4065800-4067200	Enhancers	Psoas Muscle	Psoas
46	chr11:4066000-4079200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:4066200-4067600	Weak transcription	Ovary	ovary
48	chr11:4066200-4067600	Weak transcription	HSMM	muscle
49	chr11:4066200-4068000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:4066200-4068600	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links