Variant report

Variant	rs62272190
Chromosome Location	chr3:160059767-160059768
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10513550	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920289	0.98[EUR][1000 genomes]
rs12233589	0.98[EUR][1000 genomes]
rs2275153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305401	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305406	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33999879	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736627	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773371	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806629	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41272959	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532176	0.81[ASN][1000 genomes]
rs55815116	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56119270	0.98[EUR][1000 genomes]
rs56124988	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56150006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343019	0.83[ASN][1000 genomes]
rs56401539	0.91[EUR][1000 genomes]
rs57030267	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57050097	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57277659	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57285344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57555307	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58627305	0.98[EUR][1000 genomes]
rs58654032	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58776572	0.91[EUR][1000 genomes]
rs58915028	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59695030	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59799252	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60066272	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60153357	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60222090	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60517889	0.85[AMR][1000 genomes]
rs60607858	0.91[EUR][1000 genomes]
rs60640467	0.87[AFR][1000 genomes]
rs60914777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61066536	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272169	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272171	0.84[AMR][1000 genomes]
rs62272176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272180	0.98[EUR][1000 genomes]
rs62272181	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272185	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272188	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272196	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272197	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272198	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272205	0.84[EUR][1000 genomes]
rs62272207	0.98[EUR][1000 genomes]
rs62272231	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272236	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272237	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272243	0.84[AMR][1000 genomes]
rs62272245	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272247	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272249	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62272251	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62272253	0.84[AMR][1000 genomes]
rs62272254	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272255	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272256	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272257	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272258	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272259	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272780	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272781	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272783	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272785	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272787	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272788	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272790	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272793	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62272799	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62272804	0.83[ASN][1000 genomes]
rs62272805	0.83[ASN][1000 genomes]
rs62272806	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66769612	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66850724	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68069205	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154564	0.84[AMR][1000 genomes]
rs73154582	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73154583	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73154587	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155914	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614701	0.98[EUR][1000 genomes]
rs7618017	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7645798	0.91[EUR][1000 genomes]
rs7648832	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9637414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:160025400-160073000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:160025600-160072000	Weak transcription	Thymus	Thymus
4	chr3:160025600-160073200	Weak transcription	Left Ventricle	heart
5	chr3:160034800-160082800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:160037000-160070200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:160049400-160090600	Weak transcription	NH-A	brain
8	chr3:160049800-160073200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:160050400-160064400	Weak transcription	Ovary	ovary
10	chr3:160054400-160091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:160055800-160072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:160055800-160087800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:160056000-160070600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:160056200-160075200	Weak transcription	HSMM	muscle
16	chr3:160056200-160091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:160056400-160063600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:160056400-160070200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:160056400-160072000	Weak transcription	Brain Anterior Caudate	brain
20	chr3:160056400-160073000	Weak transcription	Fetal Stomach	stomach
21	chr3:160056400-160082800	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:160056400-160098000	Weak transcription	Aorta	Aorta
23	chr3:160056600-160072000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:160056600-160072000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:160056600-160072600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:160056600-160073200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:160056600-160082400	Weak transcription	Fetal Lung	lung
28	chr3:160056600-160082800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:160056600-160083200	Weak transcription	Fetal Intestine Small	intestine
30	chr3:160056600-160091600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:160056800-160064400	Weak transcription	Primary T cells from cord blood	blood
32	chr3:160057000-160060400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:160057000-160070400	Weak transcription	Fetal Thymus	thymus
34	chr3:160057200-160072800	Weak transcription	Primary B cells from cord blood	blood
35	chr3:160057600-160060600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:160057600-160072800	Weak transcription	Fetal Intestine Large	intestine
37	chr3:160057800-160064400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:160058200-160065000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:160058400-160088800	Weak transcription	Osteobl	bone
40	chr3:160058600-160073200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:160058800-160083200	Weak transcription	GM12878-XiMat	blood
42	chr3:160059000-160072200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr3:160059000-160072800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:160059400-160059800	Enhancers	Colon Smooth Muscle	Colon
45	chr3:160059400-160077200	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links