Variant report

Variant	rs12492510
Chromosome Location	chr3:136151631-136151632
allele	G/T
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]
rs1070228	0.83[EUR][1000 genomes]
rs1070232	0.87[JPT][hapmap]
rs10804640	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935181	0.84[AMR][1000 genomes]
rs10935182	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]
rs10935183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935184	0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935186	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs1145106	0.94[JPT][hapmap]
rs1153877	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs11715257	0.94[JPT][hapmap]
rs11717954	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11719310	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11915629	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11919030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
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]
rs2688600	0.84[EUR][1000 genomes]
rs2688601	0.84[EUR][1000 genomes]
rs3755636	0.87[JPT][hapmap]
rs4678269	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4678428	0.87[JPT][hapmap]
rs4678433	0.87[JPT][hapmap]
rs4678437	0.87[JPT][hapmap]
rs4678438	0.87[JPT][hapmap]
rs483465	0.87[JPT][hapmap]
rs517319	0.85[EUR][1000 genomes]
rs518972	1.00[ASW][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]
rs521746	1.00[ASW][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs548288	0.87[JPT][hapmap]
rs553018	0.81[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap]
rs556788	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs56235965	0.85[AMR][1000 genomes]
rs571513	0.87[JPT][hapmap]
rs576771	0.81[JPT][hapmap]
rs589092	0.89[ASW][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap]
rs595532	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs606725	0.87[JPT][hapmap]
rs619605	0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs650326	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs654237	1.00[ASW][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs655748	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs655836	1.00[ASW][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs66691851	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs667920	0.87[JPT][hapmap]
rs6791611	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]
rs6794351	0.87[JPT][hapmap]
rs695983	0.94[JPT][hapmap]
rs696081	0.81[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs696516	0.94[JPT][hapmap]
rs696518	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs696520	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs698269	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs698270	0.94[JPT][hapmap]
rs699165	0.87[JPT][hapmap]
rs711972	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs711975	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs73222302	0.84[AMR][1000 genomes]
rs73226190	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7432375	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap]
rs7620314	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs7621025	0.87[JPT][hapmap]
rs833752	0.87[JPT][hapmap]
rs834304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs834305	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs864437	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs866758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs900048	0.94[JPT][hapmap]
rs940174	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9714347	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
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
rs12492510	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs12492510	PCCB	cis	cerebellum	SCAN
rs12492510	PCCB	cis	multi-tissue	Pritchard
rs12492510	PCCB	cis	parietal	SCAN
rs12492510	SPSB4	cis	cerebellum	SCAN
rs12492510	PCCB	cis	lymphoblastoid	seeQTL
rs12492510	DBR1	cis	cerebellum	SCAN

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	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:136110800-136174200	Weak transcription	Esophagus	oesophagus
8	chr3:136112200-136174200	Weak transcription	Osteobl	bone
9	chr3:136113000-136174200	Weak transcription	Aorta	Aorta
10	chr3:136114800-136160400	Weak transcription	Fetal Kidney	kidney
11	chr3:136115400-136174200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:136116200-136173400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:136116600-136174400	Weak transcription	Hela-S3	cervix
14	chr3:136118200-136170400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:136123000-136157000	Weak transcription	Colonic Mucosa	Colon
16	chr3:136124600-136174000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:136129800-136174200	Weak transcription	HSMMtube	muscle
18	chr3:136131000-136160200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:136131400-136160400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:136131400-136175400	Weak transcription	HMEC	breast
21	chr3:136133000-136160400	Weak transcription	Spleen	Spleen
22	chr3:136133200-136173800	Weak transcription	Fetal Heart	heart
23	chr3:136133600-136173400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:136135200-136173400	Weak transcription	NHEK	skin
25	chr3:136137800-136156200	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:136138200-136173600	Weak transcription	Brain Angular Gyrus	brain
27	chr3:136138400-136167000	Weak transcription	HSMM	muscle
28	chr3:136138800-136171400	Weak transcription	HepG2	liver
29	chr3:136138800-136174200	Weak transcription	Brain Anterior Caudate	brain
30	chr3:136139600-136159600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:136139800-136159600	Weak transcription	Ovary	ovary
32	chr3:136139800-136160000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:136139800-136160400	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:136139800-136160400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:136139800-136161000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:136139800-136162600	Weak transcription	Fetal Brain Male	brain
37	chr3:136139800-136163200	Weak transcription	Psoas Muscle	Psoas
38	chr3:136139800-136175400	Weak transcription	Small Intestine	intestine
39	chr3:136139800-136175800	Weak transcription	Right Ventricle	heart
40	chr3:136140000-136159400	Weak transcription	Fetal Brain Female	brain
41	chr3:136140000-136160400	Weak transcription	Gastric	stomach
42	chr3:136140000-136160400	Weak transcription	Left Ventricle	heart
43	chr3:136140000-136160400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:136140000-136160400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr3:136140000-136162800	Weak transcription	HUVEC	blood vessel
46	chr3:136140000-136168200	Weak transcription	NH-A	brain
47	chr3:136140000-136169200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:136140000-136169600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:136140000-136174200	Weak transcription	Pancreas	Pancrea
50	chr3:136140000-136175800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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