Variant report

Variant	rs12489885
Chromosome Location	chr3:196244846-196244847
allele	C/T
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	SRF	chr3:196244539-196245359	ECC-1	luminal epithelium:	n/a	chr3:196244897-196244915
2	MAX	chr3:196244809-196245053	K562	blood:	n/a	n/a
3	MAX	chr3:196244664-196245426	ECC-1	luminal epithelium:	n/a	n/a
4	SRF	chr3:196244638-196245263	ECC-1	luminal epithelium:	n/a	chr3:196244897-196244915
5	MAX	chr3:196244834-196245076	Hela-S3	cervix:	n/a	n/a
6	TCF12	chr3:196244277-196245250	ECC-1	luminal epithelium:	n/a	n/a
7	USF1	chr3:196244811-196245160	ECC-1	luminal epithelium:	n/a	n/a
8	MYC	chr3:196244826-196245071	MCF10A-Er-Src	breast:	n/a	n/a
9	YY1	chr3:196244788-196245070	K562	blood:	n/a	chr3:196244904-196244916
10	FOS	chr3:196244824-196245024	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr3:196244624-196245211	ECC-1	luminal epithelium:	n/a	n/a
12	ELK1	chr3:196244783-196245247	K562	blood:	n/a	n/a
13	FOXA1	chr3:196244752-196245053	T-47D	breast:	n/a	n/a
14	POU2F2	chr3:196244719-196245200	GM12878	blood:	n/a	chr3:196245014-196245027
15	SRF	chr3:196244796-196244981	K562	blood:	n/a	chr3:196244897-196244915
16	SRF	chr3:196244788-196244983	HepG2	liver:	n/a	chr3:196244897-196244915
17	SRF	chr3:196244814-196244986	GM12878	blood:	n/a	chr3:196244897-196244915
18	SRF	chr3:196244756-196245080	K562	blood:	n/a	chr3:196244897-196244915
19	NFIC	chr3:196244569-196245403	ECC-1	luminal epithelium:	n/a	n/a
20	CEBPB	chr3:196244764-196245090	Hela-S3	cervix:	n/a	n/a
21	SRF	chr3:196244839-196244975	GM12878	blood:	n/a	chr3:196244897-196244915
22	TCF12	chr3:196244539-196245288	ECC-1	luminal epithelium:	n/a	n/a
23	ELK1	chr3:196244805-196245111	Hela-S3	cervix:	n/a	n/a
24	MAX	chr3:196244730-196245059	K562	blood:	n/a	n/a
25	ELK4	chr3:196244738-196245078	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr3:196244200-196244956	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr3:196244757-196245119	K562	blood:	n/a	n/a
28	SRF	chr3:196244771-196244977	GM12878	blood:	n/a	chr3:196244897-196244915
29	MYC	chr3:196244815-196245017	K562	blood:	n/a	n/a
30	JUN	chr3:196243852-196246433	K562	blood:	n/a	chr3:196246149-196246162
31	SRF	chr3:196244761-196244991	HepG2	liver:	n/a	chr3:196244897-196244915
32	FOXA1	chr3:196244753-196244988	ECC-1	luminal epithelium:	n/a	n/a
33	NFIC	chr3:196244502-196245352	ECC-1	luminal epithelium:	n/a	n/a
34	YY1	chr3:196244724-196245086	H1-hESC	embryonic stem cell:	n/a	chr3:196244904-196244916
35	SRF	chr3:196244784-196244998	GM12878	blood:	n/a	chr3:196244897-196244915
36	FOXA1	chr3:196244668-196245024	T-47D	breast:	n/a	n/a
37	POU2F2	chr3:196244772-196245186	GM12891	blood:	n/a	chr3:196245014-196245027
38	YY1	chr3:196244749-196245186	H1-hESC	embryonic stem cell:	n/a	chr3:196244904-196244916

No.	Distal block	Cell Line	Cell type
1	chr3:195970824..195973413-chr3:196244591..196247031,2	K562	blood:
2	chr3:196200904..196203106-chr3:196242169..196245085,2	K562	blood:
3	chr3:195808137..195810508-chr3:196244076..196245932,2	K562	blood:

Variant related genes	Relation type
SMCO1	TF binding region
ENSG00000072274	Chromatin interaction
ENSG00000273013	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11185544	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711594	0.89[ASN][1000 genomes]
rs11711952	0.95[ASN][1000 genomes]
rs11714694	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11920455	0.92[ASN][1000 genomes]
rs12494859	0.89[ASN][1000 genomes]
rs12495687	0.89[ASN][1000 genomes]
rs2086891	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2101285	0.87[EUR][1000 genomes]
rs2341334	0.92[ASN][1000 genomes]
rs2341399	0.94[EUR][1000 genomes]
rs3964310	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4488870	0.95[ASN][1000 genomes]
rs56144237	0.92[ASN][1000 genomes]
rs57365032	0.89[ASN][1000 genomes]
rs62410583	0.89[ASN][1000 genomes]
rs6583317	0.89[ASN][1000 genomes]
rs6583318	0.89[ASN][1000 genomes]
rs66588136	0.89[ASN][1000 genomes]
rs6765975	0.95[ASN][1000 genomes]
rs6775794	0.89[ASN][1000 genomes]
rs6775806	0.95[ASN][1000 genomes]
rs6780633	0.95[ASN][1000 genomes]
rs6780856	0.95[ASN][1000 genomes]
rs6799694	0.89[ASN][1000 genomes]
rs6799697	0.82[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	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73219654	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73219660	0.95[ASN][1000 genomes]
rs7614249	0.81[ASN][1000 genomes]
rs7615547	0.95[ASN][1000 genomes]
rs7623111	0.95[ASN][1000 genomes]
rs7623224	0.89[ASN][1000 genomes]
rs7629990	0.87[ASN][1000 genomes]
rs7651365	0.81[ASN][1000 genomes]
rs9811428	0.84[ASN][1000 genomes]
rs9818507	0.95[ASN][1000 genomes]
rs9839347	0.95[ASN][1000 genomes]
rs9840938	0.95[ASN][1000 genomes]
rs9849530	0.95[ASN][1000 genomes]
rs9854347	0.85[ASN][1000 genomes]
rs9858251	0.89[ASN][1000 genomes]
rs9870613	0.89[ASN][1000 genomes]
rs9880563	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196239400-196245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:196242600-196245200	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr3:196242600-196246400	Enhancers	K562	blood
4	chr3:196244000-196245400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:196244000-196245400	Enhancers	HMEC	breast
6	chr3:196244200-196246800	Enhancers	Hela-S3	cervix
7	chr3:196244400-196245600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:196244800-196245200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr3:196244800-196247600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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