Variant report

Variant	rs6791611
Chromosome Location	chr3:136160590-136160591
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1070232	0.87[JPT][hapmap]
rs10804640	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10935181	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10935182	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]
rs10935183	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10935184	0.82[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10935186	0.92[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs1145106	0.94[JPT][hapmap]
rs1153877	0.82[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11715257	0.94[JPT][hapmap]
rs11717954	0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes]
rs11719310	0.80[AMR][1000 genomes]
rs11915629	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11919030	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs12492510	1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12630999	0.87[JPT][hapmap]
rs12635723	0.87[JPT][hapmap]
rs1279086	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1279425	0.87[JPT][hapmap]
rs1279840	0.87[JPT][hapmap]
rs1394092	0.87[JPT][hapmap]
rs1711161	0.87[JPT][hapmap]
rs1711171	0.87[JPT][hapmap]
rs2655008	0.94[JPT][hapmap]
rs3755636	0.87[JPT][hapmap]
rs4678269	0.80[AMR][1000 genomes]
rs4678428	0.87[JPT][hapmap]
rs4678433	0.87[JPT][hapmap]
rs4678437	0.87[JPT][hapmap]
rs4678438	0.87[JPT][hapmap]
rs480162	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs483465	0.87[JPT][hapmap]
rs518972	0.92[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs521746	0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs527888	0.83[EUR][1000 genomes]
rs548288	0.87[JPT][hapmap]
rs553018	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs556788	0.82[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs56235965	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs571513	0.87[JPT][hapmap]
rs576771	0.81[JPT][hapmap]
rs589092	0.92[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap]
rs595532	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs606725	0.87[JPT][hapmap]
rs619605	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs650326	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs654237	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs655748	0.81[AMR][1000 genomes]
rs655836	0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66691851	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs667920	0.87[JPT][hapmap]
rs6794351	0.87[JPT][hapmap]
rs695983	0.94[JPT][hapmap]
rs696081	1.00[ASW][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs696516	0.94[JPT][hapmap]
rs696518	0.92[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs696520	0.82[CEU][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs698269	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs698270	0.94[JPT][hapmap]
rs699165	0.87[JPT][hapmap]
rs711972	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs711975	0.84[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs73222302	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73226190	0.81[AMR][1000 genomes]
rs7432375	0.92[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs7620314	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7621025	0.87[JPT][hapmap]
rs833752	0.87[JPT][hapmap]
rs833861	0.84[EUR][1000 genomes]
rs834304	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs834305	0.81[AMR][1000 genomes]
rs864437	0.92[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs866758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs900048	0.94[JPT][hapmap]
rs940174	0.92[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs9714347	0.81[AMR][1000 genomes]
rs9845762	0.87[JPT][hapmap]
rs9854084	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6791611	BAMBI	trans	lymphoblastoid	seeQTL
rs6791611	PCCB	cis	parietal	SCAN
rs6791611	SPSB4	cis	cerebellum	SCAN
rs6791611	PCCB	cis	cerebellum	SCAN
rs6791611	DBR1	cis	cerebellum	SCAN
rs6791611	PCCB	cis	multi-tissue	Pritchard
rs6791611	PCCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 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	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:136110800-136174200	Weak transcription	Esophagus	oesophagus
6	chr3:136112200-136174200	Weak transcription	Osteobl	bone
7	chr3:136113000-136174200	Weak transcription	Aorta	Aorta
8	chr3:136115400-136174200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:136116200-136173400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:136116600-136174400	Weak transcription	Hela-S3	cervix
11	chr3:136118200-136170400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:136124600-136174000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:136129800-136174200	Weak transcription	HSMMtube	muscle
14	chr3:136131400-136175400	Weak transcription	HMEC	breast
15	chr3:136133200-136173800	Weak transcription	Fetal Heart	heart
16	chr3:136133600-136173400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:136135200-136173400	Weak transcription	NHEK	skin
18	chr3:136138200-136173600	Weak transcription	Brain Angular Gyrus	brain
19	chr3:136138400-136167000	Weak transcription	HSMM	muscle
20	chr3:136138800-136171400	Weak transcription	HepG2	liver
21	chr3:136138800-136174200	Weak transcription	Brain Anterior Caudate	brain
22	chr3:136139800-136161000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:136139800-136162600	Weak transcription	Fetal Brain Male	brain
24	chr3:136139800-136163200	Weak transcription	Psoas Muscle	Psoas
25	chr3:136139800-136175400	Weak transcription	Small Intestine	intestine
26	chr3:136139800-136175800	Weak transcription	Right Ventricle	heart
27	chr3:136140000-136162800	Weak transcription	HUVEC	blood vessel
28	chr3:136140000-136168200	Weak transcription	NH-A	brain
29	chr3:136140000-136169200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:136140000-136169600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:136140000-136174200	Weak transcription	Pancreas	Pancrea
32	chr3:136140000-136175800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:136143200-136174000	Weak transcription	GM12878-XiMat	blood
34	chr3:136148000-136174400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:136151600-136160800	Weak transcription	Lung	lung
36	chr3:136151800-136160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:136152000-136160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:136152600-136168400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:136152600-136168800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:136152600-136169000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:136156800-136166200	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:136157200-136162600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:136158000-136162600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:136158200-136161800	Strong transcription	Fetal Thymus	thymus
45	chr3:136158200-136163800	Strong transcription	Dnd41	blood
46	chr3:136158400-136169000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:136158600-136161800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr3:136158600-136162000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr3:136158600-136162200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:136158600-136162200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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