Variant report

Variant	rs12051865
Chromosome Location	chr17:20194523-20194524
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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12051550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs12051844	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16942325	0.91[CHB][hapmap]
rs16959946	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs16960700	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16960715	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16960717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16960730	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16960735	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16964352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs1971043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1971044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2526477	0.80[YRI][hapmap]
rs2703781	0.80[YRI][hapmap]
rs2703805	0.80[YRI][hapmap]
rs28550747	0.90[ASN][1000 genomes]
rs3751979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3764436	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs5025290	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[ASN][1000 genomes]
rs57110692	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61141789	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61660810	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587060	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587218	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6587221	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7207458	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7211948	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7213349	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7213816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7215097	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7215432	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7218859	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73299658	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73301548	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73309111	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73981849	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8076627	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8077051	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8077852	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9895177	0.86[ASN][1000 genomes]
rs9895295	0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9896190	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9899514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9901102	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9902683	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs9905976	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9908418	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs9911605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9913018	1.00[CHB][hapmap]
rs9913394	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9914219	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9941362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9941376	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv427993	chr17:20171398-20482061	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
18	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
19	nsv520772	chr17:20184501-20522444	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12051865	SLC47A1	cis	lymphoblastoid	seeQTL
rs12051865	CYTSB	cis	parietal	SCAN
rs12051865	ALDH3A1	cis	parietal	SCAN
rs12051865	AKAP10	cis	Whole Blood	GTEx
rs12051865	AKAP10	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20136400-20209800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:20164000-20200200	Weak transcription	Fetal Intestine Large	intestine
3	chr17:20164000-20205600	Weak transcription	Esophagus	oesophagus
4	chr17:20164200-20200200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr17:20164400-20202200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr17:20164600-20203800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:20164600-20204000	Weak transcription	Gastric	stomach
8	chr17:20167400-20200200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr17:20170400-20209600	Weak transcription	HMEC	breast
10	chr17:20171200-20200200	Weak transcription	Lung	lung
11	chr17:20173400-20197600	Weak transcription	Brain Germinal Matrix	brain
12	chr17:20174400-20200200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr17:20175000-20200200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:20180400-20200200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:20180400-20203400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:20180600-20203200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr17:20181200-20200400	Weak transcription	Adipose Nuclei	Adipose
18	chr17:20181400-20200400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:20181400-20200400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr17:20182000-20203000	Weak transcription	NH-A	brain
21	chr17:20182400-20200400	Weak transcription	Osteobl	bone
22	chr17:20184000-20200200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr17:20184800-20196000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:20184800-20200400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr17:20185000-20200200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr17:20185200-20209800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr17:20185400-20203800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:20185600-20201600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr17:20185600-20206800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr17:20185800-20203000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr17:20186000-20203000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:20186000-20209400	Weak transcription	Spleen	Spleen
33	chr17:20186200-20209800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr17:20187800-20223800	Weak transcription	Pancreas	Pancrea
35	chr17:20188000-20196000	Weak transcription	A549	lung
36	chr17:20188000-20200200	Weak transcription	Aorta	Aorta
37	chr17:20188200-20208400	Weak transcription	NHEK	skin
38	chr17:20188400-20200400	Weak transcription	HSMMtube	muscle
39	chr17:20188400-20205600	Weak transcription	Primary T cells from cord blood	blood
40	chr17:20188600-20200200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr17:20188600-20200200	Weak transcription	Brain Substantia Nigra	brain
42	chr17:20188600-20203200	Weak transcription	HSMM	muscle
43	chr17:20188600-20209800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:20188600-20209800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr17:20188800-20195800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr17:20188800-20195800	Weak transcription	Brain Hippocampus Middle	brain
47	chr17:20188800-20203000	Weak transcription	Fetal Stomach	stomach
48	chr17:20189800-20200200	Weak transcription	Brain Angular Gyrus	brain
49	chr17:20190000-20197600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:20190000-20198000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links