Variant report

Variant	rs10935182
Chromosome Location	chr3:136137422-136137423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1070232	0.93[JPT][hapmap]
rs10804640	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10935181	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10935183	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10935184	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1145106	1.00[JPT][hapmap]
rs1153877	1.00[ASW][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11715257	1.00[JPT][hapmap]
rs11717954	1.00[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11915629	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492510	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12630999	0.93[JPT][hapmap]
rs12635723	0.93[JPT][hapmap]
rs1279086	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs1279425	0.93[JPT][hapmap]
rs1279840	0.93[JPT][hapmap]
rs1394092	0.93[JPT][hapmap]
rs1711161	0.94[JPT][hapmap]
rs1711170	0.81[JPT][hapmap]
rs1711171	0.93[JPT][hapmap]
rs2655008	1.00[JPT][hapmap]
rs3755636	0.93[JPT][hapmap]
rs3957816	0.81[JPT][hapmap]
rs4678428	0.93[JPT][hapmap]
rs4678433	0.93[JPT][hapmap]
rs4678437	0.93[JPT][hapmap]
rs480162	0.90[EUR][1000 genomes]
rs483465	0.93[JPT][hapmap]
rs518972	1.00[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap]
rs521746	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs527888	0.81[EUR][1000 genomes]
rs548288	0.93[JPT][hapmap]
rs553018	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs556788	1.00[ASW][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs56235965	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs571513	0.93[JPT][hapmap]
rs576771	0.87[JPT][hapmap]
rs589092	0.89[ASW][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap]
rs595532	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs606725	0.93[JPT][hapmap]
rs619605	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs650326	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs654237	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs655748	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs655836	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs661739	0.81[JPT][hapmap]
rs66691851	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs667920	0.93[JPT][hapmap]
rs6791611	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6794351	0.93[JPT][hapmap]
rs684773	0.81[JPT][hapmap]
rs695983	1.00[JPT][hapmap]
rs696081	0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap]
rs696516	1.00[JPT][hapmap]
rs696518	1.00[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs696520	1.00[ASW][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs698269	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs698270	1.00[JPT][hapmap]
rs699165	0.93[JPT][hapmap]
rs711972	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs711975	1.00[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs73222302	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7432375	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap]
rs7620314	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[ASN][1000 genomes]
rs7621025	0.93[JPT][hapmap]
rs833752	0.93[JPT][hapmap]
rs833861	0.86[EUR][1000 genomes]
rs834304	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs834305	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs864437	1.00[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes]
rs866758	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs895894	0.81[JPT][hapmap]
rs900048	1.00[JPT][hapmap]
rs940174	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap]
rs9854084	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10935182	DBR1	cis	cerebellum	SCAN
rs10935182	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs10935182	MSL2	cis	parietal	SCAN
rs10935182	PCCB	cis	parietal	SCAN
rs10935182	PCCB	cis	lymphoblastoid	seeQTL
rs10935182	PCCB	cis	cerebellum	SCAN
rs10935182	SPSB4	cis	cerebellum	SCAN
rs10935182	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:136063600-136139200	Weak transcription	Pancreas	Pancrea
5	chr3:136069600-136138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:136069600-136139400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:136075000-136137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
10	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:136085800-136139200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:136095600-136137800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:136095800-136139200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:136096000-136138200	Weak transcription	Lung	lung
17	chr3:136104800-136139400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:136106000-136139200	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:136110000-136139000	Weak transcription	Ovary	ovary
20	chr3:136110800-136174200	Weak transcription	Esophagus	oesophagus
21	chr3:136111000-136137800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:136112200-136174200	Weak transcription	Osteobl	bone
23	chr3:136113000-136174200	Weak transcription	Aorta	Aorta
24	chr3:136114400-136139800	Weak transcription	NHDF-Ad	bronchial
25	chr3:136114800-136160400	Weak transcription	Fetal Kidney	kidney
26	chr3:136115400-136174200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:136116200-136173400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:136116600-136174400	Weak transcription	Hela-S3	cervix
29	chr3:136116800-136139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:136117400-136139200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:136118200-136170400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:136118800-136139200	Weak transcription	NHLF	lung
33	chr3:136119600-136139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:136122000-136139200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:136123000-136157000	Weak transcription	Colonic Mucosa	Colon
36	chr3:136123400-136139200	Weak transcription	HUVEC	blood vessel
37	chr3:136124000-136141600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:136124400-136139200	Weak transcription	Right Ventricle	heart
39	chr3:136124600-136174000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:136125600-136139200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:136127400-136140000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:136128200-136139200	Weak transcription	Gastric	stomach
43	chr3:136128200-136139400	Weak transcription	Small Intestine	intestine
44	chr3:136129200-136137600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:136129400-136139400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:136129800-136141400	Weak transcription	Brain Substantia Nigra	brain
47	chr3:136129800-136174200	Weak transcription	HSMMtube	muscle
48	chr3:136131000-136139200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:136131000-136160200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:136131400-136160400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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