Variant report

Variant	rs6771053
Chromosome Location	chr3:23298569-23298570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10451986	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11129112	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11129114	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11916447	0.87[ASN][1000 genomes]
rs11921580	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11928344	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12185989	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12630883	0.89[ASN][1000 genomes]
rs12632777	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12633613	0.89[ASN][1000 genomes]
rs12636682	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1495135	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17341838	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17343818	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17403650	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1908772	0.80[ASN][1000 genomes]
rs2172827	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2359637	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2359638	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28370926	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884787	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4368441	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895449	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55934161	0.80[ASN][1000 genomes]
rs57055494	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57234542	0.80[ASN][1000 genomes]
rs57624654	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57869672	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60407944	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6550761	0.80[ASN][1000 genomes]
rs6762615	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6763074	0.80[ASN][1000 genomes]
rs6764047	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6765562	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6766166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771206	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773311	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6776770	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6778478	0.81[ASN][1000 genomes]
rs6792462	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792915	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6797467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807390	0.81[ASN][1000 genomes]
rs73033545	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73033551	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7428484	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7610971	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7611132	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7613733	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7613969	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614926	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617659	0.81[ASN][1000 genomes]
rs7622913	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7630344	0.82[AFR][1000 genomes]
rs7632520	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7635784	0.89[ASN][1000 genomes]
rs7636536	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7638278	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7638405	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641764	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7646505	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7649682	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651175	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903518	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814419	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9820931	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9825835	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9835256	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839409	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9841308	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841518	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9842014	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9844723	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9845536	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881808	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9882514	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23283600-23302200	Weak transcription	Left Ventricle	heart
2	chr3:23292200-23298800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:23292800-23304200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:23292800-23306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:23293000-23298600	Weak transcription	Osteobl	bone
6	chr3:23293000-23303800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:23293200-23299400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:23294800-23299200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:23295200-23321800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:23296000-23300600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:23296000-23302000	Weak transcription	Lung	lung
12	chr3:23296400-23302000	Weak transcription	Psoas Muscle	Psoas
13	chr3:23296600-23298600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:23297000-23298800	Enhancers	Colon Smooth Muscle	Colon
15	chr3:23297000-23307000	Weak transcription	Primary B cells from cord blood	blood
16	chr3:23297600-23299000	Enhancers	Brain Hippocampus Middle	brain
17	chr3:23298000-23299000	Enhancers	Liver	Liver
18	chr3:23298000-23299800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:23298200-23298600	Enhancers	Aorta	Aorta
20	chr3:23298200-23298600	Enhancers	Brain Angular Gyrus	brain
21	chr3:23298200-23298600	Enhancers	Brain Anterior Caudate	brain
22	chr3:23298200-23298600	Enhancers	Right Atrium	heart
23	chr3:23298200-23298600	Enhancers	Stomach Smooth Muscle	stomach
24	chr3:23298200-23298600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:23298200-23298800	Enhancers	Brain Substantia Nigra	brain
26	chr3:23298200-23298800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr3:23298200-23298800	Enhancers	Rectal Smooth Muscle	rectum
28	chr3:23298200-23298800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:23298200-23298800	Enhancers	Thymus	Thymus
30	chr3:23298200-23298800	Enhancers	GM12878-XiMat	blood
31	chr3:23298200-23299000	Enhancers	Primary B cells from peripheral blood	blood
32	chr3:23298200-23299000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr3:23298200-23299000	Enhancers	Adipose Nuclei	Adipose
34	chr3:23298200-23299000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr3:23298200-23299000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:23298200-23299000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:23298200-23299000	Enhancers	A549	lung
38	chr3:23298200-23299800	Enhancers	Brain Cingulate Gyrus	brain
39	chr3:23298400-23298600	Enhancers	Fetal Kidney	kidney
40	chr3:23298400-23298600	Enhancers	Fetal Thymus	thymus
41	chr3:23298400-23298600	Enhancers	Spleen	Spleen
42	chr3:23298400-23298800	Enhancers	Fetal Heart	heart
43	chr3:23298400-23298800	Enhancers	Right Ventricle	heart
44	chr3:23298400-23298800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr3:23298400-23299200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:23298400-23300000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:23298400-23302000	Weak transcription	Pancreas	Pancrea
48	chr3:23298400-23305200	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links