Variant report

Variant	rs17562177
Chromosome Location	chr2:64160385-64160386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64160279..64161972-chr2:64164608..64167275,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10183479	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10199273	0.81[AFR][1000 genomes]
rs11558741	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11674020	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676710	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11682249	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11683408	0.90[ASN][1000 genomes]
rs11686956	0.80[ASN][1000 genomes]
rs11691987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693906	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694253	0.82[ASN][1000 genomes]
rs11695421	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713498	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12996866	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13018690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13431781	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440002	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs17562423	0.88[ASN][1000 genomes]
rs17619753	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs193031	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2302808	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439183	0.90[ASN][1000 genomes]
rs2969395	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs329478	0.90[ASN][1000 genomes]
rs329488	0.82[ASN][1000 genomes]
rs329502	0.85[CHB][hapmap]
rs34122334	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34765999	0.90[ASN][1000 genomes]
rs34777730	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs35002211	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35336851	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35474183	0.87[ASN][1000 genomes]
rs35480874	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35697586	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35960986	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36033991	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36123537	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4233930	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4538187	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671071	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671073	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs56904032	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6546029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546032	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546033	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546035	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66980330	0.98[ASN][1000 genomes]
rs6710763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6715992	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67308158	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731508	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732746	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6755646	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67615384	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67765474	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68117986	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72808243	0.98[ASN][1000 genomes]
rs72893103	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs74181291	0.80[ASN][1000 genomes]
rs7590399	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv521717	chr2:64104132-64186582	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv874236	chr2:64154215-64179235	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1002209	chr2:64160385-64238475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64114000-64212000	Weak transcription	Small Intestine	intestine
2	chr2:64114200-64174800	Weak transcription	Right Ventricle	heart
3	chr2:64129600-64164000	Weak transcription	NHLF	lung
4	chr2:64129600-64201000	Weak transcription	Hela-S3	cervix
5	chr2:64130400-64167600	Weak transcription	Fetal Heart	heart
6	chr2:64130400-64168400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:64130400-64211200	Weak transcription	Fetal Brain Male	brain
8	chr2:64130600-64168000	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:64130800-64174800	Weak transcription	Stomach Mucosa	stomach
10	chr2:64137400-64204800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:64138600-64168600	Weak transcription	Brain Angular Gyrus	brain
12	chr2:64139000-64168200	Weak transcription	Psoas Muscle	Psoas
13	chr2:64139000-64172800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:64139800-64161600	Weak transcription	HSMMtube	muscle
15	chr2:64139800-64167400	Weak transcription	NHEK	skin
16	chr2:64139800-64220600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:64140400-64187600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:64140400-64188800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:64140600-64172400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:64141200-64187600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:64141400-64167800	Weak transcription	Brain Anterior Caudate	brain
22	chr2:64141400-64189200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:64141600-64160400	Weak transcription	HUVEC	blood vessel
24	chr2:64141600-64164400	Weak transcription	Osteobl	bone
25	chr2:64141800-64160800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:64142600-64167600	Weak transcription	K562	blood
27	chr2:64142800-64189200	Weak transcription	Brain Substantia Nigra	brain
28	chr2:64143400-64167800	Weak transcription	GM12878-XiMat	blood
29	chr2:64147600-64178000	Weak transcription	A549	lung
30	chr2:64147800-64160400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr2:64147800-64160400	Weak transcription	NH-A	brain
32	chr2:64148000-64160800	Weak transcription	NHDF-Ad	bronchial
33	chr2:64148000-64164600	Weak transcription	HSMM	muscle
34	chr2:64149800-64167600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:64153600-64160800	Weak transcription	Primary T cells from cord blood	blood
36	chr2:64154400-64168400	Weak transcription	Esophagus	oesophagus
37	chr2:64154400-64168400	Weak transcription	Ovary	ovary
38	chr2:64154400-64176800	Weak transcription	Colonic Mucosa	Colon
39	chr2:64154400-64202600	Weak transcription	Spleen	Spleen
40	chr2:64154600-64160400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:64154600-64160400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:64154600-64164600	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:64154600-64165000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:64154600-64165000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:64154600-64165000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:64154600-64165200	Weak transcription	Fetal Intestine Small	intestine
47	chr2:64154600-64167800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:64154600-64167800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:64154600-64174800	Weak transcription	Thymus	Thymus
50	chr2:64154600-64202600	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links