Variant report

Variant	rs9474661
Chromosome Location	chr6:53687715-53687716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10948787	0.81[EUR][1000 genomes]
rs11759220	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11759427	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs12661475	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12661938	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12663216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1883632	0.89[CHB][hapmap]
rs3001004	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001006	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3001007	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001008	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003490	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003494	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35081045	0.81[ASN][1000 genomes]
rs3813850	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs4254992	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273680	0.80[JPT][hapmap]
rs4478409	0.86[JPT][hapmap]
rs4486000	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4540263	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4582388	0.90[ASN][1000 genomes]
rs4618525	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4645422	0.80[EUR][1000 genomes]
rs4715427	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715428	0.81[ASN][1000 genomes]
rs4715429	0.88[ASN][1000 genomes]
rs60467893	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62397076	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62397090	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6905323	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6905563	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906326	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6909040	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6909094	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6925391	0.88[ASN][1000 genomes]
rs6928222	0.82[YRI][hapmap]
rs7750173	0.95[EUR][1000 genomes]
rs9296720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9463983	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463988	0.88[ASN][1000 genomes]
rs9463996	0.94[JPT][hapmap]
rs9463997	0.89[JPT][hapmap]
rs9474643	0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs9474665	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9474661	LRRC1	cis	multi-tissue	Pritchard
rs9474661	KCNJ9	trans	parietal	SCAN
rs9474661	C6orf142	cis	cerebellum	SCAN
rs9474661	ELOVL5	cis	parietal	SCAN
rs9474661	BAG2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:53678600-53692200	Weak transcription	Esophagus	oesophagus
5	chr6:53680400-53690000	Weak transcription	Fetal Intestine Small	intestine
6	chr6:53680400-53690200	Weak transcription	Fetal Thymus	thymus
7	chr6:53680400-53691800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:53680400-53692400	Weak transcription	Pancreas	Pancrea
9	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:53680600-53689400	Weak transcription	Fetal Intestine Large	intestine
11	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:53680800-53689600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:53681200-53689800	Weak transcription	Osteobl	bone
14	chr6:53682600-53689400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:53683600-53689800	Weak transcription	Dnd41	blood
16	chr6:53684000-53691400	Weak transcription	Hela-S3	cervix
17	chr6:53684000-53692400	Weak transcription	Left Ventricle	heart
18	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
20	chr6:53684200-53689400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:53684600-53690600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
23	chr6:53684800-53688200	Enhancers	Brain Cingulate Gyrus	brain
24	chr6:53684800-53689800	Weak transcription	HMEC	breast
25	chr6:53685000-53689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:53685000-53689800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:53685000-53690200	Weak transcription	NHEK	skin
28	chr6:53685200-53688000	Enhancers	Brain Anterior Caudate	brain
29	chr6:53685600-53688400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr6:53685800-53688000	Enhancers	Brain Angular Gyrus	brain
31	chr6:53686000-53690400	Weak transcription	Gastric	stomach
32	chr6:53686200-53687800	Enhancers	Rectal Smooth Muscle	rectum
33	chr6:53686400-53688000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:53686800-53687800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr6:53686800-53688000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:53687000-53687800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:53687000-53687800	Enhancers	Fetal Brain Female	brain
38	chr6:53687000-53687800	Enhancers	HepG2	liver
39	chr6:53687200-53687800	Enhancers	H1 Cell Line	embryonic stem cell
40	chr6:53687200-53687800	Enhancers	Fetal Kidney	kidney
41	chr6:53687200-53687800	Enhancers	HSMMtube	muscle
42	chr6:53687200-53688000	Enhancers	Aorta	Aorta
43	chr6:53687200-53688000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr6:53687200-53688000	Enhancers	Fetal Muscle Leg	muscle
45	chr6:53687200-53692400	Weak transcription	Thymus	Thymus
46	chr6:53687400-53687800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:53687400-53687800	Enhancers	HSMM	muscle
48	chr6:53687400-53689400	Weak transcription	Stomach Mucosa	stomach
49	chr6:53687400-53690400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:53687400-53691600	Weak transcription	Right Atrium	heart

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