Variant report

Variant	rs12440142
Chromosome Location	chr15:56537518-56537519
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	POU2F2	chr15:56537111-56537585	GM12891	blood:	n/a	n/a
2	CHD2	chr15:56536859-56537672	GM12878	blood:	n/a	n/a
3	TCF12	chr15:56535416-56537845	A549	lung:	n/a	n/a
4	HEY1	chr15:56535842-56537705	HepG2	liver:	n/a	chr15:56536219-56536234
5	NFIC	chr15:56537059-56537645	HepG2	liver:	n/a	n/a
6	HNF4A	chr15:56537069-56537528	HepG2	liver:	n/a	chr15:56537301-56537313 chr15:56537299-56537314 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537375-56537387 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537300-56537308 chr15:56537300-56537313 chr15:56537299-56537314
7	POLR2A	chr15:56535990-56537541	GM12892	blood:	n/a	n/a
8	POLR2A	chr15:56537042-56537575	GM12878	blood:	n/a	n/a
9	ELF1	chr15:56537267-56537650	GM12878	blood:	n/a	n/a
10	TBP	chr15:56536169-56537819	HepG2	liver:	n/a	n/a
11	E2F6	chr15:56535647-56537755	K562	blood:	n/a	chr15:56536112-56536121 chr15:56535888-56535899 chr15:56535888-56535895 chr15:56535765-56535775
12	NRF1	chr15:56537504-56537930	GM12878	blood:	n/a	n/a
13	MYC	chr15:56535595-56538658	K562	blood:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512 chr15:56535837-56535847
14	RCOR1	chr15:56534834-56538657	K562	blood:	n/a	n/a
15	HNF4G	chr15:56537040-56537625	HepG2	liver:	n/a	chr15:56537301-56537313 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537375-56537387 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537300-56537308 chr15:56537300-56537315 chr15:56537300-56537313 chr15:56537299-56537314
16	MXI1	chr15:56534731-56537540	SK-N-SH	brain:	n/a	n/a
17	HEY1	chr15:56536014-56537765	HepG2	liver:	n/a	chr15:56536219-56536234
18	MAX	chr15:56535387-56537814	A549	lung:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512 chr15:56535837-56535847
19	SREBP1	chr15:56536101-56537599	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:56537320-56537551	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr15:56534851-56538643	GM12878	blood:	n/a	n/a
22	MAX	chr15:56535990-56537752	K562	blood:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512
23	NFIC	chr15:56536936-56537909	GM12878	blood:	n/a	n/a
24	MXI1	chr15:56535813-56537691	HepG2	liver:	n/a	n/a
25	TBP	chr15:56535280-56538594	K562	blood:	n/a	n/a
26	POLR2A	chr15:56537015-56537594	HepG2	liver:	n/a	n/a
27	MYBL2	chr15:56537024-56537891	HepG2	liver:	n/a	n/a
28	ARID3A	chr15:56537076-56537557	HepG2	liver:	n/a	n/a
29	HNF4G	chr15:56537030-56537624	HepG2	liver:	n/a	chr15:56537301-56537313 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537375-56537387 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537300-56537308 chr15:56537300-56537315 chr15:56537300-56537313 chr15:56537299-56537314
30	BHLHE40	chr15:56537299-56538778	GM12878	blood:	n/a	n/a
31	RUNX3	chr15:56537276-56537831	GM12878	blood:	n/a	n/a
32	HNF4A	chr15:56537105-56537559	HepG2	liver:	n/a	chr15:56537301-56537313 chr15:56537299-56537314 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537375-56537387 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537300-56537308 chr15:56537300-56537313 chr15:56537299-56537314
33	BHLHE40	chr15:56537304-56537686	K562	blood:	n/a	n/a
34	POLR2A	chr15:56535300-56538555	HepG2	liver:	n/a	n/a
35	MYC	chr15:56536641-56537675	HepG2	liver:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512
36	POLR2A	chr15:56537084-56537523	HepG2	liver:	n/a	n/a
37	MAZ	chr15:56537420-56537530	Hela-S3	cervix:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512
38	POLR2A	chr15:56536794-56537814	GM12878	blood:	n/a	n/a
39	HCFC1	chr15:56537436-56537825	K562	blood:	n/a	n/a
40	EP300	chr15:56537472-56538615	K562	blood:	n/a	chr15:56538368-56538384 chr15:56538403-56538419
41	POLR2A	chr15:56534875-56538524	GM19099	blood:	n/a	n/a
42	POLR2A	chr15:56535564-56538440	GM12892	blood:	n/a	n/a
43	RFX5	chr15:56534502-56539161	SK-N-SH	brain:	n/a	chr15:56537356-56537365 chr15:56538106-56538122
44	CEBPB	chr15:56537432-56537801	HepG2	liver:	n/a	chr15:56537605-56537616
45	TAF1	chr15:56537045-56537630	HepG2	liver:	n/a	n/a
46	CTCF	chr15:56536780-56539212	SK-N-SH	brain:	n/a	chr15:56538386-56538394 chr15:56538415-56538433 chr15:56538382-56538398 chr15:56538381-56538399 chr15:56538416-56538432 chr15:56538383-56538404
47	MYBL2	chr15:56536963-56537728	HepG2	liver:	n/a	n/a
48	POLR2A	chr15:56536917-56537703	GM12878	blood:	n/a	n/a
49	HNF4A	chr15:56537084-56537560	HepG2	liver:	n/a	chr15:56537301-56537313 chr15:56537299-56537314 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537375-56537387 chr15:56537299-56537314 chr15:56537301-56537313 chr15:56537300-56537308 chr15:56537300-56537313 chr15:56537299-56537314
50	TAF1	chr15:56537205-56537569	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:56285813..56288695-chr15:56536371..56538059,2	MCF-7	breast:
2	chr15:56535634..56538355-chr15:56656475..56659064,2	MCF-7	breast:
3	chr15:56536983..56539715-chr15:56539921..56543667,5	K562	blood:
4	chr15:56478637..56480315-chr15:56536798..56538580,2	K562	blood:
5	chr15:55834428..55836953-chr15:56536453..56538262,2	K562	blood:
6	chr15:56536601..56538445-chr15:57177718..57180315,2	K562	blood:
7	chr15:56282050..56287467-chr15:56534024..56538662,8	MCF-7	breast:
8	chr15:56483194..56486063-chr15:56535825..56539303,3	MCF-7	breast:
9	chr15:56536734..56539507-chr15:56718886..56721172,2	MCF-7	breast:
10	chr15:56536393..56538517-chr15:56614478..56617229,2	MCF-7	breast:
11	chr11:2545295..2546795-chr15:56536741..56538582,2	K562	blood:

Variant related genes	Relation type
RFX7	TF binding region
ENSG00000261174	Chromatin interaction
ENSG00000069869	Chromatin interaction
ENSG00000151575	Chromatin interaction
ENSG00000261072	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1031077	0.84[EUR][1000 genomes]
rs10851601	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10851603	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11071245	0.82[AFR][1000 genomes]
rs11071252	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11071254	0.92[EUR][1000 genomes]
rs11637507	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11637789	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12437864	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12439682	0.89[EUR][1000 genomes]
rs12439907	0.82[EUR][1000 genomes]
rs12442539	0.88[EUR][1000 genomes]
rs12443429	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12591270	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12591294	0.94[EUR][1000 genomes]
rs12592096	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12592449	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12595840	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16976760	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16976788	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16976826	0.94[EUR][1000 genomes]
rs1879348	0.87[EUR][1000 genomes]
rs4363812	0.81[EUR][1000 genomes]
rs58265497	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs59230019	0.95[EUR][1000 genomes]
rs60417530	0.85[EUR][1000 genomes]
rs68127612	0.82[AFR][1000 genomes]
rs72740505	0.95[EUR][1000 genomes]
rs748970	0.82[EUR][1000 genomes]
rs8027386	0.92[EUR][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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3388652	chr15:56534210-56537808	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	esv3377686	chr15:56534685-56537533	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56534000-56538400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr15:56534800-56538400	Active TSS	Colonic Mucosa	Colon
3	chr15:56536200-56537600	Flanking Active TSS	HSMM	muscle
4	chr15:56536200-56538400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:56536400-56538200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr15:56536400-56538200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr15:56536400-56538400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr15:56536400-56538400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:56536400-56538600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr15:56536400-56538600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:56536600-56537600	Active TSS	HepG2	liver
12	chr15:56536600-56538400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:56536600-56538600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:56536800-56537600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:56536800-56537600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:56536800-56537600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:56536800-56537800	Enhancers	Spleen	Spleen
18	chr15:56536800-56538000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:56536800-56538000	Enhancers	Fetal Heart	heart
20	chr15:56536800-56538000	Enhancers	Placenta	Placenta
21	chr15:56536800-56538200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:56536800-56538200	Flanking Active TSS	A549	lung
23	chr15:56536800-56538200	Flanking Active TSS	K562	blood
24	chr15:56536800-56538400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr15:56536800-56538400	Enhancers	Fetal Brain Male	brain
26	chr15:56536800-56538600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr15:56536800-56538600	Enhancers	Stomach Mucosa	stomach
28	chr15:56536800-56538800	Flanking Active TSS	Dnd41	blood
29	chr15:56537000-56537600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:56537000-56537600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:56537000-56537600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:56537000-56537600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:56537000-56537600	Enhancers	Gastric	stomach
34	chr15:56537000-56537600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr15:56537000-56537800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:56537000-56537800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr15:56537000-56537800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr15:56537000-56537800	Enhancers	Small Intestine	intestine
39	chr15:56537000-56538000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr15:56537000-56538000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr15:56537000-56538000	Flanking Active TSS	GM12878-XiMat	blood
42	chr15:56537000-56538200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr15:56537000-56538200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:56537000-56538200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:56537000-56538200	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr15:56537000-56538200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr15:56537000-56538200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr15:56537000-56538200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr15:56537000-56538200	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr15:56537000-56538200	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links