Variant report

Variant	rs9463983
Chromosome Location	chr6:53691679-53691680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11759220	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12661475	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12661938	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12663216	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3001004	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3001005	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3001006	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3001007	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3001008	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3003488	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3003490	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3003492	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3003494	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3003498	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35081045	0.90[ASN][1000 genomes]
rs4254992	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4486000	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4540263	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4582388	0.82[ASN][1000 genomes]
rs4618525	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4640878	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4715427	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60467893	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62397076	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62397090	0.95[EUR][1000 genomes]
rs6905323	0.95[EUR][1000 genomes]
rs6905563	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6909040	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6909094	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7750173	0.92[EUR][1000 genomes]
rs9296720	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9474661	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9474665	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9463983	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:53678600-53692200	Weak transcription	Esophagus	oesophagus
4	chr6:53680400-53691800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:53680400-53692400	Weak transcription	Pancreas	Pancrea
6	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:53684000-53692400	Weak transcription	Left Ventricle	heart
9	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
11	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
12	chr6:53687200-53692400	Weak transcription	Thymus	Thymus
13	chr6:53687600-53692400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:53687600-53693000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:53687600-53702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:53687800-53692200	Weak transcription	HSMM	muscle
17	chr6:53687800-53692800	Weak transcription	HSMMtube	muscle
18	chr6:53688000-53692000	Weak transcription	Brain Angular Gyrus	brain
19	chr6:53688000-53692400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:53688000-53694600	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:53689400-53692000	Enhancers	Colonic Mucosa	Colon
22	chr6:53689400-53692000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr6:53689400-53696400	Enhancers	Stomach Mucosa	stomach
24	chr6:53689400-53699400	Enhancers	Fetal Intestine Large	intestine
25	chr6:53689600-53694400	Enhancers	HepG2	liver
26	chr6:53689600-53695400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:53689800-53693400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:53689800-53693400	Enhancers	Small Intestine	intestine
29	chr6:53689800-53694000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:53689800-53695000	Enhancers	HMEC	breast
31	chr6:53689800-53695200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:53689800-53697200	Enhancers	Colon Smooth Muscle	Colon
33	chr6:53690000-53695400	Enhancers	Brain Cingulate Gyrus	brain
34	chr6:53690000-53699000	Enhancers	Fetal Intestine Small	intestine
35	chr6:53690200-53695000	Enhancers	Brain Hippocampus Middle	brain
36	chr6:53690200-53695600	Enhancers	NHEK	skin
37	chr6:53690400-53692000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr6:53690400-53697200	Enhancers	Brain Anterior Caudate	brain
39	chr6:53690800-53692800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:53690800-53693000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:53690800-53695200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:53691000-53691800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr6:53691000-53692200	Weak transcription	Aorta	Aorta
44	chr6:53691000-53692200	Weak transcription	Fetal Thymus	thymus
45	chr6:53691000-53692400	Enhancers	Duodenum Mucosa	Duodenum
46	chr6:53691000-53693000	Weak transcription	Gastric	stomach
47	chr6:53691200-53692200	Weak transcription	Osteobl	bone
48	chr6:53691200-53692600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr6:53691200-53697800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:53691400-53691800	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links