Variant report

Variant	rs16960717
Chromosome Location	chr17:20088289-20088290
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr17:20088252-20088720	Hela-S3	cervix:	n/a	n/a
2	EP300	chr17:20088252-20088654	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr17:20088131-20088566	K562	blood:	n/a	n/a
4	MAX	chr17:20088172-20088948	NB4	blood:	n/a	n/a
5	JUND	chr17:20088270-20088647	K562	blood:	n/a	n/a
6	SPI1	chr17:20088263-20088820	HL-60	blood:	n/a	n/a
7	MYC	chr17:20088283-20088897	K562	blood:	n/a	n/a
8	BACH1	chr17:20088046-20088596	H1-hESC	embryonic stem cell:	n/a	n/a
9	PML	chr17:20088231-20088601	K562	blood:	n/a	n/a
10	TEAD4	chr17:20088172-20088701	K562	blood:	n/a	n/a
11	TAL1	chr17:20088184-20088645	K562	blood:	n/a	n/a
12	MAFF	chr17:20088074-20088716	K562	blood:	n/a	n/a
13	GATA2	chr17:20088260-20088641	K562	blood:	n/a	n/a
14	RCOR1	chr17:20088204-20088694	K562	blood:	n/a	n/a
15	GATA3	chr17:20088111-20088810	SK-N-SH	brain:	n/a	n/a
16	MAFK	chr17:20087968-20088492	H1-hESC	embryonic stem cell:	n/a	chr17:20088136-20088147
17	IRF1	chr17:20088070-20088581	K562	blood:	n/a	chr17:20088391-20088407
18	GATA3	chr17:20088255-20088694	MCF-7	breast:	n/a	n/a
19	EP300	chr17:20088286-20088660	K562	blood:	n/a	n/a
20	GTF2F1	chr17:20088132-20088492	K562	blood:	n/a	n/a
21	CEBPB	chr17:20088237-20088616	Hela-S3	cervix:	n/a	n/a
22	BACH1	chr17:20088179-20088586	K562	blood:	n/a	n/a
23	MAFK	chr17:20088102-20088646	K562	blood:	n/a	chr17:20088136-20088147

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20080906..20083704-chr17:20086823..20088345,2	MCF-7	breast:
2	chr17:20088001..20089506-chr17:20108427..20110013,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000263494	TF binding region
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11868429	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];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12051550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12051844	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12051865	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]
rs16942325	0.91[CHB][hapmap];0.81[AMR][1000 genomes]
rs16959946	1.00[CHB][hapmap];0.88[AMR][1000 genomes]
rs16960700	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16960715	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16960735	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16964352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes]
rs1971043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1971044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28550747	0.88[AMR][1000 genomes]
rs3751979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3764436	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes]
rs5025290	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs57110692	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61141789	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61660810	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587060	0.96[EUR][1000 genomes]
rs6587061	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];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587218	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587221	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207458	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7211948	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213349	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7213816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7215097	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7215432	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7218859	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73299658	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73301548	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73309111	0.96[EUR][1000 genomes]
rs73981849	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8076627	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8077051	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8077852	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9896190	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9897161	0.88[AMR][1000 genomes]
rs9897168	0.88[AMR][1000 genomes]
rs9899514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9901102	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9901484	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9902683	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[AMR][1000 genomes]
rs9905976	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9908032	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9908418	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs9909156	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9911605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9913018	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9913394	0.89[EUR][1000 genomes]
rs9914219	0.97[EUR][1000 genomes]
rs9941362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941376	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	nsv2003	chr17:20046306-20090653	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	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
14	nsv1057870	chr17:20079146-20121848	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	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
16	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16960717	ALDH3A1	cis	parietal	SCAN
rs16960717	AKAP10	cis	Whole Blood	GTEx
rs16960717	CYTSB	cis	parietal	SCAN
rs16960717	AKAP10	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20060800-20092200	Weak transcription	Fetal Intestine Small	intestine
2	chr17:20062000-20090400	Weak transcription	Aorta	Aorta
3	chr17:20075800-20090800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:20078000-20089800	Weak transcription	Spleen	Spleen
5	chr17:20078600-20090400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr17:20079200-20088400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:20080400-20092200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:20080400-20092400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr17:20082800-20088400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:20082800-20092400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr17:20084200-20092000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:20084400-20092200	Weak transcription	Brain Germinal Matrix	brain
13	chr17:20085600-20093800	Enhancers	Brain Substantia Nigra	brain
14	chr17:20085800-20088600	Enhancers	Hela-S3	cervix
15	chr17:20085800-20089000	Enhancers	A549	lung
16	chr17:20086000-20092200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr17:20086000-20092600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr17:20086600-20092000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:20087400-20089000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:20087400-20089200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr17:20087400-20092200	Enhancers	Brain Angular Gyrus	brain
22	chr17:20087600-20088400	Enhancers	NH-A	brain
23	chr17:20087600-20088600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr17:20087600-20088600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr17:20087600-20088600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:20087600-20088600	Enhancers	Osteobl	bone
27	chr17:20087600-20088800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr17:20087600-20088800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr17:20087600-20089000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr17:20087600-20089000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr17:20087600-20089200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr17:20087600-20091400	Enhancers	Brain Anterior Caudate	brain
33	chr17:20087600-20091600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:20087600-20092200	Enhancers	Brain Cingulate Gyrus	brain
35	chr17:20087600-20092400	Enhancers	Brain Hippocampus Middle	brain
36	chr17:20087800-20088800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr17:20087800-20089000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr17:20087800-20089200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr17:20087800-20089200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:20087800-20089200	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr17:20087800-20091000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr17:20088000-20088400	Enhancers	Fetal Brain Female	brain
43	chr17:20088200-20088400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr17:20088200-20088600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:20088200-20088800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr17:20088200-20088800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr17:20088200-20088800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr17:20088200-20088800	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr17:20088200-20088800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr17:20088200-20088800	Enhancers	Ovary	ovary

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