Variant report

Variant	rs3782511
Chromosome Location	chr12:29496224-29496225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:29495805-29496815	K562	blood:	n/a	n/a

Variant related genes	Relation type
ERGIC2	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1035604	0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap]
rs10771508	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10843361	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs10843366	0.94[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10843367	0.85[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs10843371	0.84[ASN][1000 genomes]
rs10843377	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10843382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843384	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843403	0.84[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs10843425	0.84[LWK][hapmap]
rs11050161	0.84[ASN][1000 genomes]
rs11050162	0.84[ASN][1000 genomes]
rs11050167	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11050170	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050173	0.80[ASN][1000 genomes]
rs11050181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050187	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050188	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050189	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050191	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050192	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050193	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11050194	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11050208	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228468	0.81[CEU][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12231498	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12366505	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12366527	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16934135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1989478	0.80[EUR][1000 genomes]
rs2042511	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2194518	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs2194519	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[ASN][1000 genomes]
rs2194520	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs2216853	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2216854	0.95[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs3764953	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3782509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4331146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57803026	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487796	0.84[ASN][1000 genomes]
rs6487801	0.81[EUR][1000 genomes]
rs6487804	0.81[EUR][1000 genomes]
rs6487805	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67146951	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67517901	0.84[ASN][1000 genomes]
rs7139273	0.81[CEU][hapmap]
rs7294598	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7301188	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7301398	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7302129	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs7308125	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7311912	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312164	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7316004	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs737160	0.89[MEX][hapmap];0.85[TSI][hapmap]
rs7954278	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7957339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7973786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974221	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7976961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs918873	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs962866	0.81[CEU][hapmap]
rs9738721	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[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	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3782511	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
3	chr12:29470000-29500000	Weak transcription	K562	blood
4	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
6	chr12:29473800-29522600	Weak transcription	NHEK	skin
7	chr12:29476000-29502600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:29476200-29509400	Weak transcription	Spleen	Spleen
9	chr12:29476200-29512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
11	chr12:29476400-29498600	Weak transcription	Ovary	ovary
12	chr12:29476400-29509600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:29476600-29499200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:29477000-29517800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:29482000-29497200	Weak transcription	Brain Angular Gyrus	brain
18	chr12:29482200-29501400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:29483400-29518000	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
21	chr12:29485600-29533400	Weak transcription	Gastric	stomach
22	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
23	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:29487800-29501400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:29488600-29503800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:29488800-29532000	Weak transcription	NHLF	lung
27	chr12:29489200-29498800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:29489600-29497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:29489600-29500000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:29489800-29510000	Weak transcription	Brain Germinal Matrix	brain
32	chr12:29490000-29502800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
35	chr12:29490200-29502000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr12:29490200-29502200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:29490200-29506000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:29490400-29500600	Strong transcription	Dnd41	blood
39	chr12:29490400-29502800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:29490600-29502000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:29490600-29503000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr12:29491000-29499200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:29491000-29511400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:29491200-29501000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:29491200-29502600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:29491400-29506400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:29491600-29498400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:29492200-29502800	Strong transcription	Placenta	Placenta
50	chr12:29492400-29502000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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