Variant report

Variant	rs9467583
Chromosome Location	chr6:25726621-25726622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:25726265-25727575	K562	blood:	n/a	n/a
2	GTF2B	chr6:25726592-25727111	K562	blood:	n/a	n/a
3	POLR2A	chr6:25726078-25727679	K562	blood:	n/a	n/a
4	POLR2A	chr6:25726297-25727684	K562	blood:	n/a	n/a
5	CHD2	chr6:25726382-25727059	K562	blood:	n/a	n/a
6	POLR2A	chr6:25725621-25728449	K562	blood:	n/a	n/a
7	PML	chr6:25726241-25727456	K562	blood:	n/a	n/a
8	POLR2A	chr6:25726283-25728295	K562	blood:	n/a	n/a
9	MYC	chr6:25726388-25727220	K562	blood:	n/a	n/a
10	POLR2A	chr6:25726081-25727575	K562	blood:	n/a	n/a
11	POLR2A	chr6:25726276-25727598	K562	blood:	n/a	n/a
12	TBP	chr6:25726582-25727230	K562	blood:	n/a	n/a
13	CEBPD	chr6:25725966-25727592	K562	blood:	n/a	n/a
14	PML	chr6:25726167-25727552	K562	blood:	n/a	n/a
15	TAF1	chr6:25726615-25726843	K562	blood:	n/a	n/a
16	E2F6	chr6:25726542-25726889	K562	blood:	n/a	chr6:25726849-25726858
17	HEY1	chr6:25725670-25728569	K562	blood:	n/a	n/a
18	POLR2A	chr6:25725688-25728100	K562	blood:	n/a	n/a
19	BCLAF1	chr6:25725654-25727678	K562	blood:	n/a	chr6:25725790-25725799
20	TEAD4	chr6:25726357-25727486	K562	blood:	n/a	n/a
21	MYC	chr6:25726562-25727031	K562	blood:	n/a	n/a
22	NFYA	chr6:25726552-25727016	K562	blood:	n/a	chr6:25726847-25726860 chr6:25726923-25726937 chr6:25726845-25726860 chr6:25726923-25726936 chr6:25726849-25726861 chr6:25726848-25726858 chr6:25726866-25726880 chr6:25726845-25726860 chr6:25726866-25726879 chr6:25726846-25726860
23	HEY1	chr6:25726177-25727588	K562	blood:	n/a	n/a
24	CCNT2	chr6:25726618-25727172	K562	blood:	n/a	n/a
25	MAX	chr6:25726411-25726882	K562	blood:	n/a	n/a
26	POLR2A	chr6:25725813-25727544	K562	blood:	n/a	n/a
27	POLR2A	chr6:25725975-25727623	K562	blood:	n/a	n/a
28	POLR2A	chr6:25726369-25727477	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:25726597-25726647	AoSMC	blood vessel:	n/a
2	chr6:25726597-25726647	RPTEC	kidney:	n/a
3	chr6:25726597-25726647	AG09309	skin:	n/a
4	chr6:25726597-25726647	HepG2	liver:	n/a
5	chr6:25726597-25726647	SK-N-SH	brain:	n/a
6	chr6:25726597-25726647	Hela-S3	cervix:	n/a
7	chr6:25726597-25726647	HNPCEpiC	eye:	n/a
8	chr6:25726597-25726647	NH-A	brain:	n/a
9	chr6:25726597-25726647	PANC-1	pancreas:	n/a
10	chr6:25726597-25726647	HCM	heart:	n/a
11	chr6:25726597-25726647	AG04450	lung:	fetal
12	chr6:25726597-25726647	AG04449	skin:	fetal
13	chr6:25726597-25726647	K562	blood:	n/a
14	chr6:25726597-25726647	U87	brain:	n/a
15	chr6:25726597-25726647	PFSK-1	brain:	n/a
16	chr6:25726597-25726647	BJ	skin:	n/a
17	chr6:25726597-25726647	SKMC	muscle:	n/a
18	chr6:25726597-25726647	HEEpiC	esophagus:	n/a
19	chr6:25726597-25726647	HCF	heart:	n/a
20	chr6:25726597-25726647	AG10803	skin:	n/a
21	chr6:25726597-25726647	GM12892	blood:	n/a
22	chr6:25726597-25726647	GM12878	blood:	n/a
23	chr6:25726597-25726647	LNCaP	prostate:	n/a
24	chr6:25726597-25726647	ProgFib	skin:	n/a
25	chr6:25726597-25726647	MCF10A-Er-Src	breast:	n/a
26	chr6:25726597-25726647	ovcar-3	ovarian:	n/a
27	chr6:25726597-25726647	NT2-D1	testis:	n/a
28	chr6:25726597-25726647	HPAEpiC	pulmonary alveolar:	n/a
29	chr6:25726597-25726647	Jurkat	blood:	n/a
30	chr6:25726597-25726647	GM19239	blood:	n/a
31	chr6:25726597-25726647	CMK	blood:	n/a
32	chr6:25726597-25726647	GM12891	blood:	n/a
33	chr6:25726597-25726647	NB4	blood:	n/a
34	chr6:25726597-25726647	HMEC	breast:	n/a
35	chr6:25726597-25726647	ECC-1	luminal epithelium:	n/a
36	chr6:25726597-25726647	Hepatocyte	liver:	n/a
37	chr6:25726597-25726647	HEK293	kidney:	embryo
38	chr6:25726597-25726647	SK-N-SH_RA	brain:	n/a
39	chr6:25726597-25726647	IMR90	lung:	fetal
40	chr6:25726597-25726647	HRPEpiC	eye:	n/a
41	chr6:25726597-25726647	HRCEpiC	kidney:	n/a
42	chr6:25726597-25726647	A549	lung:	n/a
43	chr6:25726597-25726647	T-47D	breast:	n/a
44	chr6:25726597-25726647	HL-60	blood:	n/a
45	chr6:25726597-25726647	SAEC	small airway:	n/a
46	chr6:25726597-25726647	HCT-116	colon:	n/a
47	chr6:25726597-25726647	HRE	kidney:	n/a
48	chr6:25726597-25726647	PrEC	prostate:	n/a
49	chr6:25726597-25726647	HUVEC	blood vessel:	n/a
50	chr6:25726597-25726647	AG09319	gingival:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:25724700..25728805-chr6:26024464..26033486,16	K562	blood:
2	chr6:25725904..25728723-chr6:26024464..26030208,7	K562	blood:
3	chr6:25726594..25729863-chr6:25991893..25994558,4	K562	blood:
4	chr6:25726417..25728737-chr6:26124112..26125886,2	K562	blood:
5	chr6:25725442..25728537-chr6:25991436..25993393,3	K562	blood:
6	chr5:177631720..177633728-chr6:25726576..25729132,2	K562	blood:

No data

Variant related genes	Relation type
HIST1H2BA	TF binding region
HIST1H2BA	CpG island
ENSG00000197451	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000272462	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000124529	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10105	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11751287	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11751622	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11964886	1.00[JPT][hapmap]
rs11969868	1.00[JPT][hapmap]
rs16890970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891142	1.00[JPT][hapmap]
rs17320614	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275906	1.00[JPT][hapmap]
rs28360622	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28385589	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34438249	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34582964	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34589724	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3734524	1.00[JPT][hapmap]
rs3827502	0.82[JPT][hapmap]
rs4236039	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4343909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4351252	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906814	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6911522	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs6935084	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7746944	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771468	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7775820	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7776065	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461196	0.94[EUR][1000 genomes]
rs9461199	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467576	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467577	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467578	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467590	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885831	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9986459	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
4	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25718400-25727400	Weak transcription	HepG2	liver
2	chr6:25725800-25726800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:25726600-25726800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:25726600-25726800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:25726600-25727000	Bivalent Enhancer	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links