Variant report

Variant	rs9895618
Chromosome Location	chr17:20858920-20858921
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	CEBPB	chr17:20858775-20859084	IMR90	lung:	n/a	chr17:20858901-20858914
2	USF1	chr17:20858858-20859137	SK-N-SH_RA	brain:	n/a	n/a
3	USF2	chr17:20858842-20859145	Hela-S3	cervix:	n/a	n/a
4	USF1	chr17:20858793-20859232	A549	lung:	n/a	n/a
5	MAX	chr17:20858884-20859092	Hela-S3	cervix:	n/a	chr17:20858999-20859008 chr17:20858997-20859010
6	CEBPB	chr17:20858803-20859070	A549	lung:	n/a	chr17:20858901-20858914
7	STAT3	chr17:20858720-20859096	MCF10A-Er-Src	breast:	n/a	n/a
8	USF1	chr17:20858888-20859120	H1-hESC	embryonic stem cell:	n/a	n/a
9	RCOR1	chr17:20858876-20859036	K562	blood:	n/a	n/a
10	EP300	chr17:20858837-20859074	Hela-S3	cervix:	n/a	chr17:20858926-20858934
11	STAT3	chr17:20858722-20859038	Hela-S3	cervix:	n/a	n/a
12	STAT3	chr17:20858720-20859085	MCF10A-Er-Src	breast:	n/a	n/a
13	USF1	chr17:20858809-20859119	A549	lung:	n/a	n/a
14	USF1	chr17:20858856-20859093	H1-hESC	embryonic stem cell:	n/a	n/a
15	STAT3	chr17:20858699-20859666	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr17:20858755-20859133	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr17:20858918-20858920	K562	blood:	n/a	n/a
18	FOS	chr17:20858284-20859753	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr17:20858474-20859648	MCF10A-Er-Src	breast:	n/a	chr17:20858585-20858608
20	STAT3	chr17:20858714-20859467	MCF10A-Er-Src	breast:	n/a	n/a
21	USF1	chr17:20858848-20859055	HepG2	liver:	n/a	n/a
22	USF1	chr17:20858866-20859073	HepG2	liver:	n/a	n/a
23	USF1	chr17:20858851-20859106	SK-N-SH_RA	brain:	n/a	n/a
24	CEBPB	chr17:20858776-20859128	Hela-S3	cervix:	n/a	chr17:20858901-20858914
25	FOS	chr17:20858481-20859096	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr17:20858757-20859085	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: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10153263	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512422	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11541314	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11650653	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11869201	0.90[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]
rs11869217	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869959	0.95[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]
rs12450389	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452171	0.82[ASN][1000 genomes]
rs12937950	0.82[ASN][1000 genomes]
rs12947514	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962364	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1871275	0.82[ASN][1000 genomes]
rs2127096	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663143	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2886049	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34354508	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35022634	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4381653	0.94[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]
rs4427861	0.94[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]
rs4985942	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985945	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57522885	0.82[ASN][1000 genomes]
rs6587107	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587113	0.82[ASN][1000 genomes]
rs6587116	0.82[ASN][1000 genomes]
rs66487709	0.82[ASN][1000 genomes]
rs66516868	0.82[ASN][1000 genomes]
rs719094	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73303698	0.82[ASN][1000 genomes]
rs8072149	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080321	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs984007	0.89[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9893047	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896853	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9907786	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909279	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914758	0.89[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914916	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9895618	RP11-381P6.1	cis	Muscle Skeletal	GTEx

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	chr17:20856200-20859000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:20857800-20859200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:20857800-20859600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr17:20857800-20859800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:20857800-20859800	Enhancers	Fetal Lung	lung
16	chr17:20857800-20867600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:20858000-20859000	Enhancers	HSMMtube	muscle
18	chr17:20858000-20859200	Weak transcription	Psoas Muscle	Psoas
19	chr17:20858000-20859200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr17:20858000-20859600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr17:20858000-20859800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:20858000-20859800	Enhancers	HSMM	muscle
23	chr17:20858200-20859000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr17:20858200-20859400	Enhancers	Liver	Liver
25	chr17:20858200-20859400	Enhancers	Osteobl	bone
26	chr17:20858200-20859600	Enhancers	Fetal Intestine Large	intestine
27	chr17:20858200-20859600	Enhancers	Fetal Muscle Leg	muscle
28	chr17:20858200-20859600	Enhancers	Ovary	ovary
29	chr17:20858200-20859600	Enhancers	Pancreas	Pancrea
30	chr17:20858200-20859600	Enhancers	NHDF-Ad	bronchial
31	chr17:20858200-20860200	Enhancers	NHEK	skin
32	chr17:20858400-20859400	Enhancers	Stomach Mucosa	stomach
33	chr17:20858400-20859800	Enhancers	HMEC	breast
34	chr17:20858400-20860000	Enhancers	Colon Smooth Muscle	Colon
35	chr17:20858400-20864400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr17:20858600-20859800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:20858600-20860200	Enhancers	Hela-S3	cervix
38	chr17:20858800-20859200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr17:20858800-20859400	Enhancers	Adipose Nuclei	Adipose
40	chr17:20858800-20860200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links