Variant report

Variant	rs6583317
Chromosome Location	chr3:196260352-196260353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr3:196260253-196260646	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr3:196260204-196260617	K562	blood:	n/a	n/a
3	USF1	chr3:196259913-196260483	H1-hESC	embryonic stem cell:	n/a	n/a
4	RXRA	chr3:196260065-196260574	H1-hESC	embryonic stem cell:	n/a	n/a
5	POU5F1	chr3:196260086-196260403	H1-hESC	embryonic stem cell:	n/a	n/a
6	RXRA	chr3:196260169-196260573	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr3:196260099-196260554	H1-hESC	embryonic stem cell:	n/a	n/a
8	TEAD4	chr3:196260335-196260608	K562	blood:	n/a	n/a
9	GATA3	chr3:196260088-196260545	T-47D	breast:	n/a	n/a
10	GATA2	chr3:196260193-196260560	SH-SY5Y	brain:	n/a	n/a
11	ATF2	chr3:196259971-196260565	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr3:196259981-196260636	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr3:196260316-196260623	K562	blood:	n/a	n/a
14	ZBTB7A	chr3:196260346-196260510	K562	blood:	n/a	n/a
15	MAX	chr3:196260071-196260495	H1-hESC	embryonic stem cell:	n/a	n/a
16	NANOG	chr3:196260028-196260600	H1-hESC	embryonic stem cell:	n/a	n/a
17	ATF2	chr3:196259925-196260624	H1-hESC	embryonic stem cell:	n/a	n/a
18	BCL11A	chr3:196260111-196260415	H1-hESC	embryonic stem cell:	n/a	n/a
19	EP300	chr3:196260001-196260659	H1-hESC	embryonic stem cell:	n/a	n/a
20	REST	chr3:196260270-196260507	H1-hESC	embryonic stem cell:	n/a	n/a
21	TEAD4	chr3:196260027-196260716	H1-hESC	embryonic stem cell:	n/a	n/a
22	GATA2	chr3:196260177-196260637	HUVEC	blood vessel:	n/a	n/a
23	JUND	chr3:196259997-196260541	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr3:196260109-196260638	H1-hESC	embryonic stem cell:	n/a	n/a
25	SP1	chr3:196260008-196260494	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD2	chr3:196260172-196260585	H1-hESC	embryonic stem cell:	n/a	n/a
27	NANOG	chr3:196260262-196260472	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAL1	chr3:196260326-196260534	K562	blood:	n/a	n/a
29	SP4	chr3:196260050-196260594	H1-hESC	embryonic stem cell:	n/a	n/a
30	CEBPD	chr3:196260316-196260613	K562	blood:	n/a	n/a
31	MYC	chr3:196260346-196260555	K562	blood:	n/a	n/a
32	USF2	chr3:196260006-196260409	H1-hESC	embryonic stem cell:	n/a	n/a
33	USF1	chr3:196259849-196260403	H1-hESC	embryonic stem cell:	n/a	n/a
34	TEAD4	chr3:196259943-196260662	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr3:196259994-196260491	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:196260279-196260532	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTBP2	chr3:196260087-196260619	H1-hESC	embryonic stem cell:	n/a	n/a
38	HDAC2	chr3:196259967-196260566	H1-hESC	embryonic stem cell:	n/a	n/a
39	POU5F1	chr3:196260022-196260573	H1-hESC	embryonic stem cell:	n/a	n/a
40	CEBPB	chr3:196259843-196260535	H1-hESC	embryonic stem cell:	n/a	n/a
41	TCF12	chr3:196260108-196260415	H1-hESC	embryonic stem cell:	n/a	n/a
42	TCF12	chr3:196259997-196260560	H1-hESC	embryonic stem cell:	n/a	n/a
43	GTF2F1	chr3:196260236-196260431	H1-hESC	embryonic stem cell:	n/a	n/a
44	RCOR1	chr3:196260352-196260481	K562	blood:	n/a	n/a
45	JUND	chr3:196260058-196260465	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196259672..196262554-chr3:196667256..196669861,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000213358	TF binding region
ENSG00000225770	TF binding region
ENSG00000114503	Chromatin interaction
ENSG00000270170	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11185544	0.95[ASN][1000 genomes]
rs11706197	0.89[ASN][1000 genomes]
rs11711594	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711952	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11714694	0.95[ASN][1000 genomes]
rs11920455	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12489885	0.89[ASN][1000 genomes]
rs12494859	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495687	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054750	0.82[AMR][1000 genomes]
rs2086891	0.95[ASN][1000 genomes]
rs2341334	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2880030	0.81[AMR][1000 genomes]
rs3964310	0.95[ASN][1000 genomes]
rs4488870	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56144237	0.92[ASN][1000 genomes]
rs57365032	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410583	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583318	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66588136	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765975	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6775794	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6775806	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6780633	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6780856	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6799694	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799697	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6803397	0.87[ASN][1000 genomes]
rs6803596	0.82[ASN][1000 genomes]
rs6807081	0.84[ASN][1000 genomes]
rs6807097	0.87[ASN][1000 genomes]
rs6810083	0.84[ASN][1000 genomes]
rs73219653	0.95[ASN][1000 genomes]
rs73219654	0.95[ASN][1000 genomes]
rs73219660	0.95[ASN][1000 genomes]
rs7614249	0.81[ASN][1000 genomes]
rs7615547	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7623111	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7623224	0.89[ASN][1000 genomes]
rs7626039	0.81[AMR][1000 genomes]
rs7629990	0.87[ASN][1000 genomes]
rs7651365	0.81[ASN][1000 genomes]
rs9647412	0.85[AMR][1000 genomes]
rs9811428	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814342	0.84[ASN][1000 genomes]
rs9818507	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9831225	0.82[AMR][1000 genomes]
rs9839347	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840938	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9848622	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9849530	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9853777	0.80[AMR][1000 genomes]
rs9854347	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9858251	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868492	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9870613	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880563	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv2763750	chr3:196242261-196278366	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	47 gene(s)	inside rSNPs	diseases
11	nsv967108	chr3:196255474-196263970	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196255800-196260400	Weak transcription	HepG2	liver
2	chr3:196256200-196260800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:196259600-196261200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:196259800-196260600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:196260000-196260400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:196260000-196260600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:196260200-196260400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
8	chr3:196260200-196260600	ZNF genes & repeats	Placenta	Placenta
9	chr3:196260200-196260600	Flanking Active TSS	K562	blood
10	chr3:196260200-196261200	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links