Variant report

Variant	rs9332085
Chromosome Location	chr13:49062990-49062991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12583514	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12583617	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12583644	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12583787	1.00[ASN][1000 genomes]
rs12585384	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12585742	1.00[EUR][1000 genomes]
rs12857866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17071937	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1926597	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2148515	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3092865	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3092898	0.97[AFR][1000 genomes]
rs4151472	1.00[EUR][1000 genomes]
rs4151479	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs4151522	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4151524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs4151598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4151602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4151613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449268	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55686933	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57394470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139763	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7319276	1.00[ASN][1000 genomes]
rs7326934	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73479216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73479220	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73495016	0.87[AFR][1000 genomes]
rs73495018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73495037	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074915	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074916	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074942	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074944	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074946	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074951	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74077638	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316384	1.00[ASN][1000 genomes]
rs9316386	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9316387	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9316396	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9316398	1.00[ASN][1000 genomes]
rs9331984	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9331994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332033	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332044	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332055	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9332070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591176	1.00[ASN][1000 genomes]
rs9595914	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9595924	1.00[ASN][1000 genomes]
rs9595926	1.00[ASN][1000 genomes]

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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9332085	DSC3	trans	lymphoblastoid	seeQTL
rs9332085	HBD	trans	lymphoblastoid	seeQTL
rs9332085	ENTHD1	trans	lymphoblastoid	seeQTL
rs9332085	PRRX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49023800-49073800	Weak transcription	NH-A	brain
2	chr13:49025600-49066200	Weak transcription	Psoas Muscle	Psoas
3	chr13:49028000-49071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr13:49030600-49070600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr13:49031600-49066200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:49031800-49065400	Weak transcription	Brain Substantia Nigra	brain
7	chr13:49032000-49065600	Weak transcription	Brain Anterior Caudate	brain
8	chr13:49032000-49066200	Weak transcription	Colonic Mucosa	Colon
9	chr13:49032400-49066200	Weak transcription	Spleen	Spleen
10	chr13:49032400-49066600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:49032400-49066600	Weak transcription	Ovary	ovary
12	chr13:49032400-49067400	Weak transcription	Pancreas	Pancrea
13	chr13:49032400-49067600	Weak transcription	Gastric	stomach
14	chr13:49032800-49066200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr13:49034400-49073800	Weak transcription	Esophagus	oesophagus
16	chr13:49035200-49073400	Weak transcription	Fetal Intestine Small	intestine
17	chr13:49035600-49065400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr13:49035600-49066000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr13:49035800-49066400	Weak transcription	NHEK	skin
20	chr13:49049800-49066200	Weak transcription	Lung	lung
21	chr13:49050000-49065600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr13:49051200-49063600	Weak transcription	Primary T cells from cord blood	blood
23	chr13:49051200-49064800	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:49051800-49065400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr13:49052800-49063600	Weak transcription	Adipose Nuclei	Adipose
26	chr13:49052800-49064800	Weak transcription	Liver	Liver
27	chr13:49053200-49063800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:49053600-49063200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr13:49053600-49071200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr13:49053800-49066600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:49054200-49064800	Weak transcription	Thymus	Thymus
33	chr13:49054200-49066600	Weak transcription	Aorta	Aorta
34	chr13:49054400-49063800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr13:49054400-49064800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:49054400-49065600	Weak transcription	HUVEC	blood vessel
37	chr13:49054400-49065800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr13:49054400-49065800	Weak transcription	NHLF	lung
39	chr13:49054400-49066200	Weak transcription	Brain Angular Gyrus	brain
40	chr13:49054400-49066200	Weak transcription	Placenta	Placenta
41	chr13:49054400-49066200	Weak transcription	HSMMtube	muscle
42	chr13:49054400-49066400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:49054400-49066600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr13:49054600-49063800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr13:49054600-49063800	Weak transcription	NHDF-Ad	bronchial
46	chr13:49054600-49065600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr13:49054600-49065600	Weak transcription	Osteobl	bone
48	chr13:49054600-49066000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr13:49054600-49066200	Weak transcription	HMEC	breast
50	chr13:49055000-49065600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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