Variant report

Variant	rs4331986
Chromosome Location	chr6:53693395-53693396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10948783	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10948784	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12193567	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12194768	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12209621	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3935664	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4128619	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236114	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4260754	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4265034	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4273680	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4392712	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4583974	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4612163	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4645423	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458967	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458968	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6904545	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910777	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6913431	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935621	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935838	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7453639	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7745548	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749635	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7749749	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7751036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7755924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761285	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9296722	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9296723	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9349682	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349683	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349684	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9367543	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9370234	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9370237	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9370238	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370240	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9382240	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382242	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382243	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs9382245	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382247	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382254	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs9395879	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9395880	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9395882	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395883	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9395884	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9395887	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4331986	LRRC1	cis	parietal	SCAN
rs4331986	ELOVL5	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
7	chr6:53687600-53702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:53688000-53694600	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:53689400-53696400	Enhancers	Stomach Mucosa	stomach
10	chr6:53689400-53699400	Enhancers	Fetal Intestine Large	intestine
11	chr6:53689600-53694400	Enhancers	HepG2	liver
12	chr6:53689600-53695400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:53689800-53693400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:53689800-53693400	Enhancers	Small Intestine	intestine
15	chr6:53689800-53694000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:53689800-53695000	Enhancers	HMEC	breast
17	chr6:53689800-53695200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:53689800-53697200	Enhancers	Colon Smooth Muscle	Colon
19	chr6:53690000-53695400	Enhancers	Brain Cingulate Gyrus	brain
20	chr6:53690000-53699000	Enhancers	Fetal Intestine Small	intestine
21	chr6:53690200-53695000	Enhancers	Brain Hippocampus Middle	brain
22	chr6:53690200-53695600	Enhancers	NHEK	skin
23	chr6:53690400-53697200	Enhancers	Brain Anterior Caudate	brain
24	chr6:53690800-53695200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:53691200-53697800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:53691400-53695000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:53691400-53697400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:53691600-53693600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:53691600-53693600	Enhancers	NHLF	lung
30	chr6:53691800-53693400	Enhancers	HUVEC	blood vessel
31	chr6:53691800-53695200	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr6:53692000-53693800	Enhancers	Brain Angular Gyrus	brain
33	chr6:53692000-53694400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:53692000-53696000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr6:53692200-53693400	Enhancers	Esophagus	oesophagus
36	chr6:53692200-53693400	Enhancers	HSMM	muscle
37	chr6:53692200-53693400	Enhancers	Osteobl	bone
38	chr6:53692200-53694000	Enhancers	Fetal Thymus	thymus
39	chr6:53692200-53694000	Enhancers	Right Atrium	heart
40	chr6:53692400-53693400	Enhancers	Left Ventricle	heart
41	chr6:53692400-53693400	Enhancers	Pancreas	Pancrea
42	chr6:53692400-53693400	Enhancers	Thymus	Thymus
43	chr6:53692400-53694000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:53692400-53694000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:53692400-53694400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:53692400-53695000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:53692400-53695600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr6:53692400-53696600	Enhancers	Placenta Amnion	Placenta Amnion
49	chr6:53692400-53697800	Weak transcription	Brain Germinal Matrix	brain
50	chr6:53692600-53693400	Enhancers	Rectal Smooth Muscle	rectum

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