Variant report

Variant	rs73411525
Chromosome Location	chr15:56537652-56537653
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	CHD2	chr15:56536859-56537672	GM12878	blood:	n/a	n/a
2	TCF12	chr15:56535416-56537845	A549	lung:	n/a	n/a
3	HEY1	chr15:56535842-56537705	HepG2	liver:	n/a	chr15:56536219-56536234
4	POLR2A	chr15:56537549-56538433	GM12892	blood:	n/a	n/a
5	POLR2A	chr15:56537639-56537655	MCF-7	breast:	n/a	n/a
6	TBP	chr15:56536169-56537819	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:56537631-56537688	K562	blood:	n/a	n/a
8	E2F6	chr15:56535647-56537755	K562	blood:	n/a	chr15:56536112-56536121 chr15:56535888-56535899 chr15:56535888-56535895 chr15:56535765-56535775
9	NRF1	chr15:56537504-56537930	GM12878	blood:	n/a	n/a
10	MYC	chr15:56535595-56538658	K562	blood:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512 chr15:56535837-56535847
11	RCOR1	chr15:56534834-56538657	K562	blood:	n/a	n/a
12	HEY1	chr15:56536014-56537765	HepG2	liver:	n/a	chr15:56536219-56536234
13	MAX	chr15:56535387-56537814	A549	lung:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512 chr15:56535837-56535847
14	POLR2A	chr15:56534851-56538643	GM12878	blood:	n/a	n/a
15	MAX	chr15:56535990-56537752	K562	blood:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512
16	NFIC	chr15:56536936-56537909	GM12878	blood:	n/a	n/a
17	MXI1	chr15:56535813-56537691	HepG2	liver:	n/a	n/a
18	TBP	chr15:56535280-56538594	K562	blood:	n/a	n/a
19	MYBL2	chr15:56537024-56537891	HepG2	liver:	n/a	n/a
20	CTCF	chr15:56537580-56537730	NHDF-neo	bronchial:	n/a	n/a
21	BHLHE40	chr15:56537299-56538778	GM12878	blood:	n/a	n/a
22	RUNX3	chr15:56537276-56537831	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr15:56537567-56538601	GM12878	blood:	n/a	n/a
24	BHLHE40	chr15:56537304-56537686	K562	blood:	n/a	n/a
25	POLR2A	chr15:56535300-56538555	HepG2	liver:	n/a	n/a
26	MYC	chr15:56536641-56537675	HepG2	liver:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512
27	POLR2A	chr15:56536794-56537814	GM12878	blood:	n/a	n/a
28	HCFC1	chr15:56537436-56537825	K562	blood:	n/a	n/a
29	EP300	chr15:56537472-56538615	K562	blood:	n/a	chr15:56538368-56538384 chr15:56538403-56538419
30	POLR2A	chr15:56534875-56538524	GM19099	blood:	n/a	n/a
31	POLR2A	chr15:56535564-56538440	GM12892	blood:	n/a	n/a
32	RFX5	chr15:56534502-56539161	SK-N-SH	brain:	n/a	chr15:56537356-56537365 chr15:56538106-56538122
33	CEBPB	chr15:56537432-56537801	HepG2	liver:	n/a	chr15:56537605-56537616
34	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
35	MYBL2	chr15:56536963-56537728	HepG2	liver:	n/a	n/a
36	POLR2A	chr15:56536917-56537703	GM12878	blood:	n/a	n/a
37	MAZ	chr15:56537120-56537747	HepG2	liver:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512
38	POLR2A	chr15:56535648-56538710	GM12878	blood:	n/a	n/a
39	JUND	chr15:56535506-56538596	K562	blood:	n/a	chr15:56536926-56536934 chr15:56535841-56535850 chr15:56537355-56537364
40	MYC	chr15:56535576-56537838	K562	blood:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512 chr15:56535837-56535847
41	PML	chr15:56536782-56538717	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:56536162-56537827	HepG2	liver:	n/a	n/a
43	POLR2A	chr15:56535061-56538547	GM12892	blood:	n/a	n/a
44	TBP	chr15:56537089-56538551	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:56535034-56538561	GM15510	blood:	n/a	n/a
46	CEBPB	chr15:56537430-56539012	K562	blood:	n/a	chr15:56538784-56538797 chr15:56538666-56538679 chr15:56537605-56537616 chr15:56538786-56538795 chr15:56538784-56538795 chr15:56538785-56538796
47	POLR2A	chr15:56535480-56538543	K562	blood:	n/a	n/a
48	MTA3	chr15:56536940-56538686	GM12878	blood:	n/a	n/a
49	MAZ	chr15:56534851-56537737	K562	blood:	n/a	chr15:56537486-56537493 chr15:56537485-56537494 chr15:56537502-56537512 chr15:56535837-56535847 chr15:56535242-56535252
50	STAT3	chr15:56537634-56537795	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:56285427..56286973-chr15:56537527..56538833,7	MCF-7	breast:
2	chr15:56285813..56288695-chr15:56536371..56538059,2	MCF-7	breast:
3	chr15:56535634..56538355-chr15:56656475..56659064,2	MCF-7	breast:
4	chr15:56536983..56539715-chr15:56539921..56543667,5	K562	blood:
5	chr15:56478637..56480315-chr15:56536798..56538580,2	K562	blood:
6	chr15:55834428..55836953-chr15:56536453..56538262,2	K562	blood:
7	chr15:56536601..56538445-chr15:57177718..57180315,2	K562	blood:
8	chr15:56282050..56287467-chr15:56534024..56538662,8	MCF-7	breast:
9	chr15:56483194..56486063-chr15:56535825..56539303,3	MCF-7	breast:
10	chr15:56536734..56539507-chr15:56718886..56721172,2	MCF-7	breast:
11	chr15:56536393..56538517-chr15:56614478..56617229,2	MCF-7	breast:
12	chr11:2545295..2546795-chr15:56536741..56538582,2	K562	blood:

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10851602	1.00[AMR][1000 genomes]
rs1372751	1.00[AMR][1000 genomes]
rs2034019	1.00[AMR][1000 genomes]
rs2584688	1.00[AMR][1000 genomes]
rs2713942	1.00[AMR][1000 genomes]
rs4774234	1.00[AMR][1000 genomes]
rs4774846	1.00[AMR][1000 genomes]
rs55968075	1.00[AMR][1000 genomes]
rs56824866	1.00[AMR][1000 genomes]
rs58771650	1.00[AMR][1000 genomes]
rs61181469	1.00[AMR][1000 genomes]
rs7171270	1.00[AMR][1000 genomes]
rs7178214	1.00[AMR][1000 genomes]
rs73411509	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411519	1.00[AMR][1000 genomes]
rs73411529	1.00[AMR][1000 genomes]
rs73413930	1.00[AMR][1000 genomes]
rs73413935	1.00[AMR][1000 genomes]
rs73413939	1.00[AMR][1000 genomes]
rs73413960	1.00[AMR][1000 genomes]
rs73413962	1.00[AMR][1000 genomes]
rs73413974	1.00[AMR][1000 genomes]
rs73413982	1.00[AMR][1000 genomes]
rs8025379	1.00[AMR][1000 genomes]
rs8030570	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8032923	1.00[AMR][1000 genomes]
rs8036425	1.00[AMR][1000 genomes]
rs8042687	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:119 , 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	chr15:56536200-56538400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:56536400-56538200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr15:56536400-56538200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr15:56536400-56538400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr15:56536400-56538400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:56536400-56538600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr15:56536400-56538600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:56536600-56538400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:56536600-56538600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:56536800-56537800	Enhancers	Spleen	Spleen
13	chr15:56536800-56538000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:56536800-56538000	Enhancers	Fetal Heart	heart
15	chr15:56536800-56538000	Enhancers	Placenta	Placenta
16	chr15:56536800-56538200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:56536800-56538200	Flanking Active TSS	A549	lung
18	chr15:56536800-56538200	Flanking Active TSS	K562	blood
19	chr15:56536800-56538400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr15:56536800-56538400	Enhancers	Fetal Brain Male	brain
21	chr15:56536800-56538600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr15:56536800-56538600	Enhancers	Stomach Mucosa	stomach
23	chr15:56536800-56538800	Flanking Active TSS	Dnd41	blood
24	chr15:56537000-56537800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:56537000-56537800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr15:56537000-56537800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr15:56537000-56537800	Enhancers	Small Intestine	intestine
28	chr15:56537000-56538000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr15:56537000-56538000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr15:56537000-56538000	Flanking Active TSS	GM12878-XiMat	blood
31	chr15:56537000-56538200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr15:56537000-56538200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:56537000-56538200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:56537000-56538200	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr15:56537000-56538200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:56537000-56538200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr15:56537000-56538200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr15:56537000-56538200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr15:56537000-56538200	Enhancers	Lung	lung
40	chr15:56537000-56538200	Flanking Active TSS	Hela-S3	cervix
41	chr15:56537000-56538400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr15:56537000-56538400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr15:56537000-56538400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:56537000-56538400	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr15:56537000-56538400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr15:56537000-56538400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr15:56537000-56538400	Flanking Active TSS	HMEC	breast
48	chr15:56537000-56538600	Enhancers	Esophagus	oesophagus
49	chr15:56537000-56538600	Enhancers	Fetal Muscle Leg	muscle
50	chr15:56537000-56538600	Flanking Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links