Variant report

Variant	rs7750173
Chromosome Location	chr6:53748170-53748171
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10948787	0.86[EUR][1000 genomes]
rs11751301	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11759220	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11759427	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs12661475	0.95[EUR][1000 genomes]
rs12661938	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12663216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13437448	0.82[EUR][1000 genomes]
rs1883632	0.89[CHB][hapmap];0.82[CHD][hapmap]
rs2050159	0.90[ASN][1000 genomes]
rs2076496	0.84[EUR][1000 genomes]
rs2076497	0.83[EUR][1000 genomes]
rs3001004	0.95[EUR][1000 genomes]
rs3001005	0.95[EUR][1000 genomes]
rs3001006	0.95[EUR][1000 genomes]
rs3001007	0.95[EUR][1000 genomes]
rs3001008	0.95[EUR][1000 genomes]
rs3003488	0.95[EUR][1000 genomes]
rs3003490	0.95[EUR][1000 genomes]
rs3003492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs3003494	0.95[EUR][1000 genomes]
rs3003498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs3813850	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs4254992	0.95[EUR][1000 genomes]
rs4273680	0.80[JPT][hapmap]
rs4478409	0.86[JPT][hapmap]
rs4486000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs4540263	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4618525	0.95[EUR][1000 genomes]
rs4640878	0.95[EUR][1000 genomes]
rs4712050	0.84[EUR][1000 genomes]
rs4712051	0.82[EUR][1000 genomes]
rs4715427	0.90[EUR][1000 genomes]
rs5006063	0.83[EUR][1000 genomes]
rs60467893	0.92[EUR][1000 genomes]
rs61068246	0.83[EUR][1000 genomes]
rs62396285	0.82[EUR][1000 genomes]
rs62397076	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62397090	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6905323	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6905563	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes]
rs6906326	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs6909040	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6909094	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6916929	0.93[ASN][1000 genomes]
rs6927232	0.82[EUR][1000 genomes]
rs763813	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs763815	0.82[EUR][1000 genomes]
rs9296720	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9296727	0.82[EUR][1000 genomes]
rs9463983	0.92[EUR][1000 genomes]
rs9463996	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9463997	0.89[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs9474643	0.82[CHB][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap]
rs9474661	0.95[EUR][1000 genomes]
rs9474665	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9474671	0.92[ASN][1000 genomes]
rs9474687	0.83[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	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	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7750173	ELOVL5	cis	parietal	SCAN
rs7750173	C6orf142	cis	cerebellum	SCAN
rs7750173	BAG2	cis	cerebellum	SCAN
rs7750173	BCL7A	trans	lymphoblastoid	seeQTL
rs7750173	KCNJ9	trans	parietal	SCAN
rs7750173	LRRC1	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
4	chr6:53730200-53748200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
6	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
7	chr6:53735000-53751800	Weak transcription	Gastric	stomach
8	chr6:53735400-53755600	Weak transcription	HUVEC	blood vessel
9	chr6:53736200-53751400	Weak transcription	Brain Substantia Nigra	brain
10	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
11	chr6:53739000-53753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:53739000-53753600	Weak transcription	NHEK	skin
13	chr6:53739000-53767800	Weak transcription	Ovary	ovary
14	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
15	chr6:53740000-53750600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:53740000-53752400	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:53740000-53755200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:53740400-53754000	Weak transcription	HSMM	muscle
19	chr6:53740400-53761000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:53741800-53760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:53742200-53760800	Weak transcription	Fetal Intestine Large	intestine
22	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
23	chr6:53742400-53758800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:53743000-53761800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:53744000-53762400	Weak transcription	Placenta	Placenta
26	chr6:53744200-53752200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:53744400-53748200	Weak transcription	Dnd41	blood
28	chr6:53744600-53764200	Weak transcription	Fetal Intestine Small	intestine
29	chr6:53744800-53752200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:53744800-53760400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:53745400-53760600	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:53745600-53762200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:53746200-53757200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:53746200-53758000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:53746400-53758600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:53746400-53762000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:53746800-53762000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr6:53746800-53768400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:53747000-53753600	Weak transcription	HMEC	breast
40	chr6:53747400-53751600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:53747600-53767800	Weak transcription	Small Intestine	intestine
42	chr6:53747800-53748400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:53747800-53748800	Enhancers	HSMMtube	muscle
44	chr6:53747800-53749200	Strong transcription	Primary T cells from cord blood	blood
45	chr6:53747800-53749200	Strong transcription	Fetal Thymus	thymus
46	chr6:53748000-53749000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr6:53748000-53750600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:53748000-53750600	Strong transcription	HepG2	liver

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