Variant report

Variant	rs12490276
Chromosome Location	chr3:196230974-196230975
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	POLR2A	chr3:196229718-196231036	Raji	blood:	n/a	n/a
2	MAZ	chr3:196229283-196231121	IMR90	lung:	n/a	n/a
3	CREB1	chr3:196229609-196231008	GM12878	blood:	n/a	n/a
4	HDAC2	chr3:196230345-196230981	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:196229560-196231038	MCF10A-Er-Src	breast:	n/a	n/a
6	CREB1	chr3:196230269-196230995	ECC-1	luminal epithelium:	n/a	n/a
7	RFX5	chr3:196229552-196231300	Hela-S3	cervix:	n/a	n/a
8	NFIC	chr3:196229404-196230988	ECC-1	luminal epithelium:	n/a	n/a
9	GABPA	chr3:196229653-196231133	MCF-7	breast:	n/a	chr3:196230569-196230578 chr3:196230736-196230745 chr3:196230489-196230496
10	GABPA	chr3:196230139-196231008	K562	blood:	n/a	chr3:196230569-196230578 chr3:196230736-196230745 chr3:196230489-196230496
11	POLR2A	chr3:196229648-196231278	HepG2	liver:	n/a	n/a
12	SIN3AK20	chr3:196229410-196231010	MCF-7	breast:	n/a	n/a
13	TCF12	chr3:196230261-196231023	A549	lung:	n/a	n/a
14	CREB1	chr3:196230317-196230983	H1-hESC	embryonic stem cell:	n/a	n/a
15	SPI1	chr3:196230068-196231038	GM12878	blood:	n/a	chr3:196230485-196230498 chr3:196230486-196230499 chr3:196230487-196230496
16	GABPA	chr3:196230137-196230983	SK-N-SH	brain:	n/a	chr3:196230569-196230578 chr3:196230736-196230745 chr3:196230489-196230496
17	CREB1	chr3:196229626-196230980	K562	blood:	n/a	n/a
18	RPC155	chr3:196230715-196231499	Hela-S3	cervix:	n/a	n/a
19	JUN	chr3:196229516-196231018	K562	blood:	n/a	chr3:196230737-196230746
20	E2F6	chr3:196229693-196231085	A549	lung:	n/a	chr3:196230541-196230551 chr3:196230656-196230667 chr3:196230672-196230683 chr3:196230659-196230667 chr3:196230660-196230667 chr3:196230208-196230215 chr3:196230659-196230667 chr3:196230569-196230578 chr3:196230657-196230668 chr3:196230733-196230742 chr3:196230658-196230668 chr3:196230659-196230667
21	TAF1	chr3:196230072-196230983	ECC-1	luminal epithelium:	n/a	n/a
22	EP300	chr3:196229518-196231012	ECC-1	luminal epithelium:	n/a	chr3:196230720-196230727 chr3:196230421-196230437 chr3:196230736-196230745
23	FOXM1	chr3:196230158-196231039	ECC-1	luminal epithelium:	n/a	n/a
24	BCLAF1	chr3:196230124-196231022	GM12878	blood:	n/a	chr3:196230347-196230360 chr3:196230469-196230482
25	RUNX3	chr3:196229377-196231058	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:196229545-196231026	GM18505	blood:	n/a	n/a
27	POLR2A	chr3:196229948-196230986	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:196230261-196231013	HepG2	liver:	n/a	n/a
29	ZNF143	chr3:196230358-196230985	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr3:196229529-196231185	SK-N-MC	brain:	n/a	n/a
31	MTA3	chr3:196229347-196231118	GM12878	blood:	n/a	n/a
32	ELF1	chr3:196230128-196230977	K562	blood:	n/a	chr3:196230464-196230476 chr3:196230720-196230729 chr3:196230487-196230496 chr3:196230719-196230730 chr3:196230719-196230730
33	POLR2A	chr3:196230222-196231018	U87	brain:	n/a	n/a
34	ELF1	chr3:196230189-196230983	SK-N-SH	brain:	n/a	chr3:196230464-196230476 chr3:196230720-196230729 chr3:196230487-196230496 chr3:196230719-196230730 chr3:196230719-196230730
35	YY1	chr3:196230185-196231001	HepG2	liver:	n/a	chr3:196230427-196230438 chr3:196230612-196230623
36	RCOR1	chr3:196229738-196231080	K562	blood:	n/a	n/a
37	TCF12	chr3:196229436-196231037	ECC-1	luminal epithelium:	n/a	n/a
38	RCOR1	chr3:196229863-196231011	K562	blood:	n/a	n/a
39	TBP	chr3:196229599-196231053	K562	blood:	n/a	n/a
40	ELF1	chr3:196230133-196231042	GM12878	blood:	n/a	chr3:196230464-196230476 chr3:196230720-196230729 chr3:196230487-196230496 chr3:196230719-196230730 chr3:196230719-196230730
41	ELF1	chr3:196230055-196231062	MCF-7	breast:	n/a	chr3:196230464-196230476 chr3:196230720-196230729 chr3:196230487-196230496 chr3:196230719-196230730 chr3:196230719-196230730
42	POLR2A	chr3:196229451-196231028	GM12891	blood:	n/a	n/a
43	POLR2A	chr3:196229803-196230995	H1-hESC	embryonic stem cell:	n/a	n/a
44	CREB1	chr3:196229573-196231140	GM12878	blood:	n/a	n/a
45	TCF7L2	chr3:196229106-196230996	Hela-S3	cervix:	n/a	n/a
46	FOXA1	chr3:196230370-196230983	HepG2	liver:	n/a	n/a
47	POLR2A	chr3:196229901-196231028	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr3:196230196-196231063	HUVEC	blood vessel:	n/a	n/a
49	TCF12	chr3:196229458-196231031	ECC-1	luminal epithelium:	n/a	n/a
50	ZBTB7A	chr3:196230241-196231010	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:196014537..196016415-chr3:196229117..196231929,2	MCF-7	breast:
2	chr3:196228328..196231500-chr3:196241253..196244010,3	MCF-7	breast:
3	chr3:195808495..195810108-chr3:196228997..196231874,2	K562	blood:
4	chr3:196062616..196065996-chr3:196228027..196230994,3	K562	blood:
5	chr3:196230868..196233512-chr3:196236802..196239351,2	K562	blood:
6	chr3:195808373..195809995-chr3:196228997..196231632,2	K562	blood:
7	chr3:196228489..196231887-chr3:196292830..196296417,3	MCF-7	breast:
8	chr3:196156342..196159977-chr3:196227568..196231019,3	MCF-7	breast:
9	chr3:196228351..196232071-chr3:196294107..196297178,4	MCF-7	breast:
10	chr3:196064683..196067033-chr3:196229952..196232006,2	K562	blood:
11	chr3:196014550..196016725-chr3:196229110..196232092,4	K562	blood:

Variant related genes	Relation type
RNF168	TF binding region
ENSG00000273331	Chromatin interaction
ENSG00000163960	Chromatin interaction
ENSG00000214097	Chromatin interaction
ENSG00000225822	Chromatin interaction
ENSG00000072274	Chromatin interaction
ENSG00000161217	Chromatin interaction
ENSG00000174013	Chromatin interaction
ENSG00000145107	Chromatin interaction
ENSG00000185798	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11185544	0.81[ASN][1000 genomes]
rs11711952	0.81[ASN][1000 genomes]
rs11714694	0.81[ASN][1000 genomes]
rs2086891	0.81[ASN][1000 genomes]
rs3964310	0.81[ASN][1000 genomes]
rs4488870	0.81[ASN][1000 genomes]
rs56144237	0.84[ASN][1000 genomes]
rs6765975	0.81[ASN][1000 genomes]
rs6775806	0.81[ASN][1000 genomes]
rs6780633	0.81[ASN][1000 genomes]
rs6780856	0.81[ASN][1000 genomes]
rs6803397	0.89[ASN][1000 genomes]
rs6803596	0.84[ASN][1000 genomes]
rs6807081	0.87[ASN][1000 genomes]
rs6807097	0.84[ASN][1000 genomes]
rs6810083	0.87[ASN][1000 genomes]
rs73219653	0.81[ASN][1000 genomes]
rs73219654	0.81[ASN][1000 genomes]
rs73219660	0.81[ASN][1000 genomes]
rs7615547	0.81[ASN][1000 genomes]
rs7623111	0.81[ASN][1000 genomes]
rs7629990	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9818507	0.81[ASN][1000 genomes]
rs9839347	0.81[ASN][1000 genomes]
rs9840938	0.81[ASN][1000 genomes]
rs9849530	0.81[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	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196225800-196231600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:196226400-196231000	Active TSS	GM12878-XiMat	blood
3	chr3:196226400-196231200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:196226800-196231200	Active TSS	Colonic Mucosa	Colon
5	chr3:196227000-196231000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr3:196227000-196231000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:196227000-196231000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:196227000-196231000	Active TSS	Esophagus	oesophagus
9	chr3:196227000-196231200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr3:196227000-196231200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:196227000-196231200	Active TSS	Fetal Kidney	kidney
12	chr3:196227000-196231200	Active TSS	Rectal Smooth Muscle	rectum
13	chr3:196227200-196231000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:196227200-196231000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:196227200-196231000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:196227200-196231000	Active TSS	Lung	lung
17	chr3:196227200-196231000	Active TSS	HMEC	breast
18	chr3:196227200-196231200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:196227200-196231200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr3:196227200-196231200	Active TSS	Brain Angular Gyrus	brain
21	chr3:196227200-196231400	Active TSS	Fetal Muscle Trunk	muscle
22	chr3:196227200-196231600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:196227400-196231000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:196227400-196231000	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:196227400-196231000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:196227400-196231000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:196227400-196231000	Active TSS	Aorta	Aorta
28	chr3:196227400-196231000	Active TSS	Colon Smooth Muscle	Colon
29	chr3:196227400-196231000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr3:196227400-196231000	Active TSS	Fetal Brain Male	brain
31	chr3:196227400-196231000	Active TSS	Fetal Intestine Small	intestine
32	chr3:196227400-196231000	Active TSS	Fetal Lung	lung
33	chr3:196227400-196231000	Active TSS	Fetal Stomach	stomach
34	chr3:196227400-196231000	Active TSS	Ovary	ovary
35	chr3:196227400-196231000	Active TSS	A549	lung
36	chr3:196227400-196231000	Active TSS	Hela-S3	cervix
37	chr3:196227400-196231000	Active TSS	HSMM	muscle
38	chr3:196227400-196231000	Active TSS	HSMMtube	muscle
39	chr3:196227400-196231000	Active TSS	NHDF-Ad	bronchial
40	chr3:196227400-196231000	Active TSS	NHLF	lung
41	chr3:196227400-196231200	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr3:196227400-196231200	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr3:196227400-196231200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:196227400-196231200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:196227400-196231200	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr3:196227400-196231200	Active TSS	Muscle Satellite Cultured Cells	--
47	chr3:196227400-196231200	Active TSS	Psoas Muscle	Psoas
48	chr3:196227400-196231200	Active TSS	Right Ventricle	heart
49	chr3:196227400-196231200	Active TSS	NH-A	brain
50	chr3:196227400-196231400	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links