Variant report

Variant	rs742524
Chromosome Location	chr6:53791217-53791218
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	JUND	chr6:53791191-53791844	HCT-116	colon:	n/a	n/a
2	NFIC	chr6:53791078-53792454	ECC-1	luminal epithelium:	n/a	chr6:53792271-53792287 chr6:53792270-53792287
3	TCF12	chr6:53791149-53792460	ECC-1	luminal epithelium:	n/a	chr6:53792118-53792125
4	MAFK	chr6:53791137-53791276	HepG2	liver:	n/a	n/a
5	EP300	chr6:53791203-53792612	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:53791111..53793110-chr6:53802444..53804078,2	MCF-7	breast:
2	chr6:53658327..53660153-chr6:53789681..53791376,2	MCF-7	breast:
3	chr6:53656777..53661250-chr6:53790077..53794763,7	MCF-7	breast:
4	chr6:53669263..53671782-chr6:53791090..53793404,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236740	TF binding region
MLIP	TF binding region
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10948779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13220665	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2745461	0.97[EUR][1000 genomes]
rs2745462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2820215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2820216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs3000997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3000999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3001001	0.81[AMR][1000 genomes]
rs3001009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3003493	1.00[CEU][hapmap]
rs3813849	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs4236113	1.00[CEU][hapmap]
rs4236115	0.86[EUR][1000 genomes]
rs4351263	1.00[CEU][hapmap]
rs4489155	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs4715424	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs6458969	0.83[AMR][1000 genomes]
rs6458971	0.89[EUR][1000 genomes]
rs6458972	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6901644	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6924025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7759946	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs7774173	0.86[EUR][1000 genomes]
rs9296721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9367544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9370239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9382234	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs9382250	0.88[EUR][1000 genomes]
rs9395886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs9474694	1.00[CHB][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv3346482	chr6:53788493-53791691	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv3361290	chr6:53788943-53791441	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
2	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
4	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:53772000-53803000	Weak transcription	Lung	lung
7	chr6:53778000-53791800	Weak transcription	Small Intestine	intestine
8	chr6:53779600-53791400	Weak transcription	Placenta	Placenta
9	chr6:53783000-53791400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:53784600-53791600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:53784600-53794200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:53784800-53794000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:53785600-53791400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:53785600-53794400	Weak transcription	Thymus	Thymus
15	chr6:53786000-53791800	Weak transcription	Fetal Stomach	stomach
16	chr6:53786000-53794200	Weak transcription	Left Ventricle	heart
17	chr6:53786600-53791400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:53786600-53791600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:53786800-53791400	Weak transcription	Fetal Kidney	kidney
20	chr6:53786800-53794400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:53787600-53791400	Weak transcription	Fetal Intestine Small	intestine
22	chr6:53787600-53791400	Weak transcription	Osteobl	bone
23	chr6:53787800-53791400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:53787800-53791400	Weak transcription	Fetal Intestine Large	intestine
25	chr6:53787800-53791600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:53787800-53793600	Weak transcription	HepG2	liver
27	chr6:53787800-53794400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:53787800-53794400	Weak transcription	Pancreas	Pancrea
29	chr6:53787800-53794800	Weak transcription	Spleen	Spleen
30	chr6:53787800-53796000	Weak transcription	Primary T cells from cord blood	blood
31	chr6:53787800-53807800	Weak transcription	Aorta	Aorta
32	chr6:53787800-53810800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:53788000-53791600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:53788000-53794400	Weak transcription	Primary B cells from cord blood	blood
35	chr6:53789400-53792600	Enhancers	Stomach Mucosa	stomach
36	chr6:53789600-53792800	Enhancers	Dnd41	blood
37	chr6:53790000-53791400	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr6:53790200-53791400	Enhancers	Esophagus	oesophagus
39	chr6:53790200-53791600	Enhancers	HSMMtube	muscle
40	chr6:53790400-53791600	Enhancers	Gastric	stomach
41	chr6:53790400-53792200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr6:53790400-53793000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr6:53790600-53797200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:53790600-53798000	Weak transcription	Fetal Thymus	thymus
45	chr6:53790800-53791400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
46	chr6:53790800-53792400	Enhancers	Fetal Heart	heart
47	chr6:53790800-53792400	Enhancers	Fetal Muscle Leg	muscle
48	chr6:53790800-53793000	Enhancers	HMEC	breast
49	chr6:53790800-53794800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:53790800-53795000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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