Variant report

Variant	rs189671
Chromosome Location	chr2:62959308-62959309
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10153716	0.89[EUR][1000 genomes]
rs1022110	0.92[CEU][hapmap]
rs11682530	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11688816	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11893131	0.96[CEU][hapmap]
rs12328837	0.93[JPT][hapmap]
rs12713467	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713468	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12713469	0.85[CHB][hapmap]
rs12989754	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12994674	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13013218	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1386399	0.87[JPT][hapmap]
rs1420018	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1487074	0.93[JPT][hapmap]
rs1534418	0.87[JPT][hapmap]
rs1534420	0.87[JPT][hapmap]
rs1553832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17027429	0.92[CEU][hapmap]
rs1828398	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1872789	0.87[JPT][hapmap]
rs1872790	0.93[JPT][hapmap]
rs1906198	0.87[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2058566	0.82[ASN][1000 genomes]
rs2080227	0.81[CEU][hapmap]
rs2136737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2204655	0.87[JPT][hapmap]
rs2204656	0.87[JPT][hapmap]
rs2215870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2421816	0.87[CEU][hapmap]
rs2430388	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2539985	0.83[ASN][1000 genomes]
rs2539987	0.96[CEU][hapmap];0.94[CHB][hapmap]
rs2710638	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2710639	0.85[CEU][hapmap]
rs2710640	0.83[ASN][1000 genomes]
rs2710642	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34104251	0.89[EUR][1000 genomes]
rs360797	0.92[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs360799	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360800	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360801	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs360804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360807	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360808	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs3927201	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4461246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671050	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4671051	0.81[EUR][1000 genomes]
rs4671448	0.90[CHB][hapmap]
rs4671450	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545968	0.93[JPT][hapmap]
rs6545969	0.93[JPT][hapmap]
rs6545971	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6545972	0.92[CEU][hapmap]
rs6545973	0.87[CEU][hapmap]
rs6705835	0.93[JPT][hapmap]
rs6757128	0.93[JPT][hapmap]
rs7557501	0.92[CEU][hapmap]
rs7562149	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7567923	0.92[CEU][hapmap]
rs7573756	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9678329	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9973612	0.96[CEU][hapmap];0.88[EUR][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	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62950600-62960600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:62952800-62960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:62953600-63001200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:62953800-62969200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:62956800-62959600	ZNF genes & repeats	A549	lung
6	chr2:62957800-62959400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:62957800-62960400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:62958200-62959400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:62958200-62959600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:62958200-62959800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:62958200-62959800	Weak transcription	HSMM	muscle
12	chr2:62958200-62960200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:62958200-62960200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:62958200-62960400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:62958200-62960600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:62958200-62960600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:62958200-62960600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:62958200-62960600	Weak transcription	NHLF	lung
19	chr2:62958200-62960800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:62958200-62960800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:62958200-62960800	Weak transcription	Aorta	Aorta
22	chr2:62958200-62960800	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:62958200-62960800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:62958200-62960800	Weak transcription	Osteobl	bone
25	chr2:62958200-62961000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:62958200-62961000	Weak transcription	Hela-S3	cervix
27	chr2:62958200-62961800	Weak transcription	Ovary	ovary
28	chr2:62958200-62962000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:62958200-62964000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:62958200-62964000	Weak transcription	Stomach Mucosa	stomach
31	chr2:62958200-62964000	Weak transcription	K562	blood
32	chr2:62958200-62964400	Weak transcription	Small Intestine	intestine
33	chr2:62958200-62964600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:62958200-62964600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:62958200-62965000	Weak transcription	Lung	lung
36	chr2:62958200-62966000	Weak transcription	HUVEC	blood vessel
37	chr2:62958200-62967400	Weak transcription	Fetal Heart	heart
38	chr2:62958200-62968000	Weak transcription	Left Ventricle	heart
39	chr2:62958200-62969200	Weak transcription	HSMMtube	muscle
40	chr2:62958200-62969200	Weak transcription	NH-A	brain
41	chr2:62958200-62970600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:62958200-62971800	Weak transcription	Gastric	stomach
43	chr2:62958200-62975000	Weak transcription	Pancreas	Pancrea
44	chr2:62958200-62981400	Weak transcription	Fetal Stomach	stomach
45	chr2:62958200-62981600	Weak transcription	Esophagus	oesophagus
46	chr2:62958200-62982800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:62958200-63010200	Weak transcription	Primary B cells from cord blood	blood
48	chr2:62958600-62959600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:62958600-62960400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:62958600-62960800	Weak transcription	Liver	Liver

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