Variant report

Variant	rs2923953
Chromosome Location	chr11:4045757-4045758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10742223	0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10767807	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11030394	0.87[AFR][1000 genomes]
rs11030536	0.89[AFR][1000 genomes]
rs11030842	0.86[CHB][hapmap]
rs11030853	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11030907	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11604649	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12364664	0.93[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12419208	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12799265	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12803023	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1372804	0.86[CHB][hapmap]
rs1372805	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2304891	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2412344	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2920139	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920143	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923944	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2923945	0.83[AMR][1000 genomes]
rs2923950	0.87[EUR][1000 genomes]
rs2958713	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2958714	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2959056	0.81[CHB][hapmap]
rs2959065	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2959066	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2959068	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2959070	0.87[CHB][hapmap]
rs2959074	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2959075	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2959079	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs61188043	0.83[AFR][1000 genomes]
rs7102508	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7110060	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7116520	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7124301	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs747883	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9704047	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][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	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2923953	RRM1	cis	Artery Tibial	GTEx
rs2923953	STIM1	cis	lung	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4038000-4049400	Weak transcription	Spleen	Spleen
2	chr11:4038200-4048800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:4038200-4057200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:4038200-4065200	Weak transcription	Left Ventricle	heart
5	chr11:4038400-4065400	Weak transcription	Esophagus	oesophagus
6	chr11:4038800-4050000	Weak transcription	K562	blood
7	chr11:4039200-4056400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:4040200-4046800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:4040200-4049600	Weak transcription	A549	lung
10	chr11:4040400-4046200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:4041000-4046600	Weak transcription	NHEK	skin
12	chr11:4041200-4046000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:4041400-4046200	Weak transcription	NHDF-Ad	bronchial
14	chr11:4041600-4046000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:4041600-4046800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:4041800-4054600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:4042000-4046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:4042000-4046000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:4043400-4047000	Strong transcription	Primary T cells from cord blood	blood
20	chr11:4043400-4051200	Weak transcription	Liver	Liver
21	chr11:4043600-4046400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:4043600-4046400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:4043600-4048000	Strong transcription	Thymus	Thymus
24	chr11:4043600-4049400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:4043800-4046000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:4043800-4046000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:4044000-4045800	ZNF genes & repeats	GM12878-XiMat	blood
28	chr11:4044000-4046000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr11:4044000-4048200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr11:4044200-4045800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr11:4044200-4047000	Weak transcription	Osteobl	bone
32	chr11:4044200-4047200	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:4044200-4050200	Strong transcription	Fetal Thymus	thymus
34	chr11:4044400-4046400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:4044400-4048200	Strong transcription	Dnd41	blood
36	chr11:4044400-4049200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr11:4044600-4046400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:4044600-4048000	Weak transcription	Small Intestine	intestine
39	chr11:4044800-4045800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:4044800-4046600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:4044800-4049000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:4045000-4046000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
43	chr11:4045000-4046200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:4045000-4046200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr11:4045000-4046400	Strong transcription	HepG2	liver
46	chr11:4045000-4047800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:4045000-4048400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:4045000-4048400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr11:4045000-4048400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr11:4045000-4049000	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links