Variant report

Variant	rs16962469
Chromosome Location	chr17:20858432-20858433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr17:20858284-20859753	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-5	chr17:20857205-20859807	NONHSAT146865

Variant related genes	Relation type
ENSG00000233098	TF binding region
ENSG00000244456	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1045215	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs10512423	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap]
rs11204325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204326	0.94[JPT][hapmap]
rs11204327	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204329	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11541311	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11650623	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11651078	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11651500	0.81[AMR][1000 genomes]
rs11652224	0.81[AMR][1000 genomes]
rs11653213	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11653504	0.81[AMR][1000 genomes]
rs11654801	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes]
rs11655512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11656525	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11656662	0.85[AMR][1000 genomes]
rs11658178	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes]
rs11658389	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11658671	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11658722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11658791	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11869271	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11870338	1.00[CHB][hapmap]
rs16942330	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[AMR][1000 genomes]
rs16962375	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16962470	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2009757	0.80[ASN][1000 genomes]
rs2291035	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap]
rs3785544	0.85[AMR][1000 genomes]
rs3891644	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4545877	0.94[JPT][hapmap]
rs4985937	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985938	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985939	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985940	0.94[JPT][hapmap]
rs4985943	0.86[ASN][1000 genomes]
rs4985944	0.82[ASN][1000 genomes]
rs62055504	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62055511	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62056764	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62056765	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62056768	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62056770	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62056771	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62056832	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs716959	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs7215006	0.94[JPT][hapmap]
rs7216145	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7217797	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7218520	0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs7221189	0.90[ASN][1000 genomes]
rs7226143	0.87[ASN][1000 genomes]
rs7501525	0.85[ASN][1000 genomes]
rs8079468	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs8080233	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9896109	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9905095	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.82[ASN][1000 genomes]
rs9914432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972887	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv3330516	chr17:20572433-20862663	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv574597	chr17:20802778-20872331	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv527161	chr17:20814766-20872331	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv457706	chr17:20814766-20872331	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv574598	chr17:20814766-20872331	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
10	nsv2006	chr17:20846763-20892730	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20835600-20869000	Weak transcription	HepG2	liver
2	chr17:20847800-20869400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:20848200-20859400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr17:20848200-20860600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr17:20848200-20864600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:20848200-20872200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:20848200-20896600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:20848400-20865000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr17:20852800-20882600	Weak transcription	K562	blood
10	chr17:20855200-20860200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:20856200-20858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:20856200-20858800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:20856200-20859000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:20857800-20859200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:20857800-20859600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr17:20857800-20859800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:20857800-20859800	Enhancers	Fetal Lung	lung
18	chr17:20857800-20867600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:20858000-20858800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:20858000-20859000	Enhancers	HSMMtube	muscle
21	chr17:20858000-20859200	Weak transcription	Psoas Muscle	Psoas
22	chr17:20858000-20859200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr17:20858000-20859600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr17:20858000-20859800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:20858000-20859800	Enhancers	HSMM	muscle
26	chr17:20858200-20858800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:20858200-20859000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr17:20858200-20859400	Enhancers	Liver	Liver
29	chr17:20858200-20859400	Enhancers	Osteobl	bone
30	chr17:20858200-20859600	Enhancers	Fetal Intestine Large	intestine
31	chr17:20858200-20859600	Enhancers	Fetal Muscle Leg	muscle
32	chr17:20858200-20859600	Enhancers	Ovary	ovary
33	chr17:20858200-20859600	Enhancers	Pancreas	Pancrea
34	chr17:20858200-20859600	Enhancers	NHDF-Ad	bronchial
35	chr17:20858200-20860200	Enhancers	NHEK	skin
36	chr17:20858400-20858800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr17:20858400-20859400	Enhancers	Stomach Mucosa	stomach
38	chr17:20858400-20859800	Enhancers	HMEC	breast
39	chr17:20858400-20860000	Enhancers	Colon Smooth Muscle	Colon
40	chr17:20858400-20864400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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