Variant report

Variant	rs16964352
Chromosome Location	chr17:20148408-20148409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11868429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs12051550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12051865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs13339684	0.83[EUR][1000 genomes]
rs16942325	0.90[CEU][hapmap];0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16959946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16960660	0.84[EUR][1000 genomes]
rs16960678	0.84[EUR][1000 genomes]
rs16960717	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes]
rs16960730	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs1971043	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs1971044	1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs28550747	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28567541	0.84[EUR][1000 genomes]
rs28622601	0.84[EUR][1000 genomes]
rs28644386	0.83[EUR][1000 genomes]
rs3751979	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs3764436	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5025290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56138907	0.84[EUR][1000 genomes]
rs57110692	0.84[ASN][1000 genomes]
rs61660810	0.90[ASN][1000 genomes]
rs6587061	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs7207458	0.92[ASN][1000 genomes]
rs7210439	0.84[EUR][1000 genomes]
rs7213816	1.00[CHB][hapmap]
rs7215097	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs7225605	0.84[EUR][1000 genomes]
rs73981803	0.84[EUR][1000 genomes]
rs73981807	0.84[EUR][1000 genomes]
rs73981849	0.86[AMR][1000 genomes]
rs73984564	0.83[EUR][1000 genomes]
rs73984568	0.83[EUR][1000 genomes]
rs73984571	0.84[EUR][1000 genomes]
rs73984573	0.84[EUR][1000 genomes]
rs8077852	0.82[ASN][1000 genomes]
rs9889684	0.82[EUR][1000 genomes]
rs9895177	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9895295	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap]
rs9897161	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9897168	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9899514	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9901102	0.84[ASN][1000 genomes]
rs9901357	0.84[EUR][1000 genomes]
rs9901484	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9902683	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9908032	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9908418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9909156	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9911605	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs9911879	0.84[EUR][1000 genomes]
rs9913018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9916729	0.84[EUR][1000 genomes]
rs9941362	1.00[CHB][hapmap]
rs9941376	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
14	nsv1065363	chr17:20118499-20162888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1059774	chr17:20118499-20163560	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv1062124	chr17:20139384-20206601	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv543261	chr17:20139384-20206601	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
19	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16964352	AKAP10	cis	multi-tissue	Pritchard
rs16964352	ALDH3A1	cis	parietal	SCAN
rs16964352	CYTSB	cis	parietal	SCAN
rs16964352	AKAP10	cis	Whole Blood	GTEx
rs16964352	USP32P3	cis	Nerve Tibial	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20111600-20166000	Weak transcription	Right Ventricle	heart
2	chr17:20128800-20157000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:20129200-20161600	Weak transcription	Fetal Brain Female	brain
4	chr17:20129600-20161600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:20130600-20161200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr17:20130600-20170000	Weak transcription	K562	blood
7	chr17:20130600-20170200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr17:20131800-20164400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr17:20132600-20151200	Weak transcription	NH-A	brain
10	chr17:20134400-20150200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr17:20134800-20150000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:20136000-20149400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr17:20136000-20151400	Weak transcription	Brain Germinal Matrix	brain
14	chr17:20136000-20151400	Weak transcription	Esophagus	oesophagus
15	chr17:20136200-20148600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr17:20136200-20149400	Weak transcription	Fetal Intestine Small	intestine
17	chr17:20136200-20151200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:20136200-20151200	Weak transcription	Colonic Mucosa	Colon
19	chr17:20136200-20151200	Weak transcription	GM12878-XiMat	blood
20	chr17:20136200-20157200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr17:20136200-20161600	Weak transcription	Lung	lung
22	chr17:20136400-20149800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr17:20136400-20151200	Weak transcription	Pancreas	Pancrea
24	chr17:20136400-20151400	Weak transcription	Left Ventricle	heart
25	chr17:20136400-20160800	Weak transcription	Fetal Stomach	stomach
26	chr17:20136400-20161200	Weak transcription	Fetal Lung	lung
27	chr17:20136400-20209800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr17:20136600-20149400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:20137400-20149200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr17:20137600-20149200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:20137600-20151000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr17:20138200-20148600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr17:20138200-20157400	Weak transcription	Gastric	stomach
34	chr17:20138400-20149400	Weak transcription	Aorta	Aorta
35	chr17:20138400-20151400	Weak transcription	NHEK	skin
36	chr17:20138400-20165200	Weak transcription	Primary B cells from cord blood	blood
37	chr17:20138600-20148600	Weak transcription	A549	lung
38	chr17:20138600-20149200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr17:20138600-20149400	Weak transcription	HSMMtube	muscle
40	chr17:20138600-20151200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:20138800-20148600	Weak transcription	Spleen	Spleen
42	chr17:20138800-20151200	Weak transcription	Fetal Intestine Large	intestine
43	chr17:20139000-20148600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr17:20139000-20149600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:20139200-20148800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr17:20139400-20148600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr17:20139400-20149000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr17:20139600-20149400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:20139600-20151200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr17:20139600-20151200	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links