Variant report

Variant	rs56827347
Chromosome Location	chr4:95376163-95376164
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	POLR2A	chr4:95372105-95377374	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr4:95376152-95376391	K562	blood:	n/a	n/a
3	RAD21	chr4:95376051-95376644	IMR90	lung:	n/a	n/a
4	CEBPB	chr4:95375707-95376698	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr4:95375984-95376661	A549	lung:	n/a	n/a
6	MYC	chr4:95375992-95376751	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr4:95376091-95376665	HepG2	liver:	n/a	n/a
8	POLR2A	chr4:95372198-95377263	MCF10A-Er-Src	breast:	n/a	n/a
9	TEAD4	chr4:95376056-95376676	HepG2	liver:	n/a	n/a
10	ARID3A	chr4:95376080-95376685	HepG2	liver:	n/a	chr4:95376277-95376293
11	MAFK	chr4:95376068-95376599	IMR90	lung:	n/a	chr4:95376141-95376156
12	CEBPB	chr4:95376082-95376640	K562	blood:	n/a	n/a
13	EP300	chr4:95375625-95376680	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr4:95376131-95376184	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr4:95375975-95376699	IMR90	lung:	n/a	n/a
16	MYC	chr4:95376045-95376642	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr4:95375968-95376168	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95373418..95376357-chr4:95500477..95502998,3	K562	blood:

Variant related genes	Relation type
ENSG00000203436	TF binding region
PDLIM5	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11097429	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11097430	0.91[AMR][1000 genomes]
rs11932136	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11932224	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11933735	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11935012	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11935039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11935084	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11935947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11938329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11938449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11939756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11940613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11941259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11941353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11942920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11946663	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58528979	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6845473	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874705	1.00[EUR][1000 genomes]
rs72874730	1.00[EUR][1000 genomes]
rs72874733	1.00[EUR][1000 genomes]
rs72874739	1.00[EUR][1000 genomes]
rs72874745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874752	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874760	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874764	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874769	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874781	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72874802	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876211	1.00[EUR][1000 genomes]
rs72876216	1.00[EUR][1000 genomes]
rs72876217	1.00[EUR][1000 genomes]
rs72876219	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876229	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72876241	1.00[EUR][1000 genomes]
rs72890408	1.00[EUR][1000 genomes]
rs72890416	1.00[EUR][1000 genomes]
rs7673478	1.00[EUR][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	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95372000-95376400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:95372000-95376600	Active TSS	Stomach Smooth Muscle	stomach
3	chr4:95372000-95376600	Active TSS	HSMMtube	muscle
4	chr4:95372000-95376800	Active TSS	A549	lung
5	chr4:95372200-95376200	Active TSS	Psoas Muscle	Psoas
6	chr4:95372200-95376600	Active TSS	NHLF	lung
7	chr4:95372200-95376800	Active TSS	Ovary	ovary
8	chr4:95372200-95378200	Active TSS	Left Ventricle	heart
9	chr4:95372200-95378200	Active TSS	Right Atrium	heart
10	chr4:95372200-95378200	Active TSS	Right Ventricle	heart
11	chr4:95372400-95376400	Active TSS	Fetal Muscle Leg	muscle
12	chr4:95372400-95376600	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr4:95372400-95377000	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr4:95372400-95377200	Active TSS	Aorta	Aorta
15	chr4:95372600-95376200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:95372600-95376400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:95372600-95376600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:95372600-95376800	Active TSS	Duodenum Mucosa	Duodenum
19	chr4:95372600-95377000	Active TSS	K562	blood
20	chr4:95372800-95376400	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr4:95372800-95376600	Active TSS	HMEC	breast
22	chr4:95373400-95376200	ZNF genes & repeats	Fetal Heart	heart
23	chr4:95373800-95376400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:95374200-95376600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:95374200-95377200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:95374200-95378800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:95374200-95387000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:95374200-95388600	Weak transcription	Gastric	stomach
29	chr4:95374200-95389200	Weak transcription	Lung	lung
30	chr4:95374200-95395400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:95374200-95400000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:95374400-95376400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr4:95374400-95376600	Active TSS	GM12878-XiMat	blood
34	chr4:95374400-95382400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:95374600-95376400	Flanking Active TSS	Osteobl	bone
36	chr4:95374600-95376800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr4:95374600-95378800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr4:95374600-95378800	Weak transcription	Pancreas	Pancrea
39	chr4:95374600-95379000	Weak transcription	Thymus	Thymus
40	chr4:95374600-95380200	Weak transcription	Primary B cells from cord blood	blood
41	chr4:95374600-95381000	Weak transcription	Spleen	Spleen
42	chr4:95374600-95382200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:95374600-95388800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:95374800-95377000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:95374800-95378800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr4:95374800-95378800	Weak transcription	Small Intestine	intestine
47	chr4:95374800-95380600	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr4:95374800-95381600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:95374800-95385200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:95374800-95398200	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links