Variant report

Variant	rs3094296
Chromosome Location	chr3:101400167-101400168
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	chr3:101400099-101400944	K562	blood:	n/a	n/a
2	POLR2A	chr3:101398386-101400417	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:101400123-101400831	K562	blood:	n/a	n/a
4	POLR2A	chr3:101398301-101401459	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:101395783-101401679	K562	blood:	n/a	n/a
6	POLR2A	chr3:101400161-101400845	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:101399847-101400869	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:101400097-101400454	U87	brain:	n/a	n/a
9	POLR2A	chr3:101400110-101400842	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:101398391-101401007	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:101398199-101400566	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr3:101400081-101400815	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr3:101394548-101402463	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:101400015-101400902	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:101400118-101400454	U87	brain:	n/a	n/a
16	POLR2A	chr3:101398409-101401956	K562	blood:	n/a	n/a
17	POLR2A	chr3:101399285-101400820	MCF-7	breast:	n/a	n/a
18	POLR2A	chr3:101399878-101400736	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr3:101400160-101401630	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr3:101400069-101400707	U87	brain:	n/a	n/a
21	POLR2A	chr3:101400158-101400497	HCT-116	colon:	n/a	n/a
22	POLR2A	chr3:101398382-101400948	GM12891	blood:	n/a	n/a
23	POLR2A	chr3:101400074-101400459	GM12892	blood:	n/a	n/a
24	POLR2A	chr3:101394775-101400361	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr3:101398557-101400845	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:101397333-101400882	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr3:101398426-101400920	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ZBTB11	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1031710	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056579	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1138818	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11706986	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707250	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap]
rs11710533	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710805	0.84[ASN][1000 genomes]
rs11711079	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711903	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap]
rs11712309	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11712748	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714278	0.89[ASN][1000 genomes]
rs11714444	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs11717046	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717638	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11718446	0.81[JPT][hapmap]
rs11720745	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914318	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11917569	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917682	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919389	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11924013	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11925001	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629658	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629954	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12633089	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs12635128	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636557	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639028	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060963	0.87[ASN][1000 genomes]
rs13061565	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065944	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[ASN][1000 genomes]
rs13066768	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs13068350	0.81[ASN][1000 genomes]
rs13069443	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077703	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077925	0.91[ASN][1000 genomes]
rs13081846	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082236	0.84[EUR][1000 genomes]
rs13084113	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13085776	0.92[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs13094753	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs13096323	0.82[ASN][1000 genomes]
rs13099674	0.91[ASN][1000 genomes]
rs13100262	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1460097	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap]
rs17345528	0.95[JPT][hapmap]
rs17347156	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs17411983	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963961	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963962	0.91[ASN][1000 genomes]
rs2288272	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290859	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs2303474	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.91[ASN][1000 genomes]
rs3094295	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094297	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109756	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34181125	0.91[ASN][1000 genomes]
rs34301719	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34376498	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.91[ASN][1000 genomes]
rs34624546	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34883763	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35117343	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35850993	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36002990	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36060163	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762729	0.95[JPT][hapmap]
rs3804775	0.95[JPT][hapmap]
rs3804778	0.95[JPT][hapmap]
rs3806653	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806654	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3864012	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4342086	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap]
rs55654108	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55859364	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56291106	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59596156	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282218	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282255	0.81[ASN][1000 genomes]
rs62284162	0.82[EUR][1000 genomes]
rs62284198	0.91[ASN][1000 genomes]
rs62284199	0.91[ASN][1000 genomes]
rs71625262	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629753	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645391	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651406	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651721	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830943	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997739	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3094296	LOC285359	cis	brain	BrainEAC
rs3094296	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101396400-101401200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:101396400-101402800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:101397000-101400400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:101397000-101400400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:101397000-101402400	Weak transcription	Fetal Brain Male	brain
6	chr3:101397000-101402600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:101397200-101400800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr3:101397200-101402600	Weak transcription	Right Atrium	heart
9	chr3:101397200-101402600	Weak transcription	Right Ventricle	heart
10	chr3:101397200-101402800	Weak transcription	Fetal Heart	heart
11	chr3:101397400-101400200	Weak transcription	Small Intestine	intestine
12	chr3:101397400-101402000	Strong transcription	Fetal Intestine Small	intestine
13	chr3:101397800-101400200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:101398400-101401200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:101398400-101402000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:101398400-101402000	Strong transcription	Fetal Brain Female	brain
17	chr3:101398400-101402200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:101398400-101402600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:101398400-101402600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:101398400-101402800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:101398400-101403400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:101398600-101400600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:101398600-101400600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:101398600-101401400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:101398600-101401600	Strong transcription	A549	lung
26	chr3:101398600-101402200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:101398600-101402200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:101398600-101402200	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:101398600-101402200	Strong transcription	Hela-S3	cervix
30	chr3:101398600-101402600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr3:101398600-101402600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:101398600-101402600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:101398600-101402600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:101398600-101402600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr3:101398600-101402600	Strong transcription	Fetal Lung	lung
36	chr3:101398600-101402600	Strong transcription	Placenta	Placenta
37	chr3:101398600-101402600	Strong transcription	Fetal Thymus	thymus
38	chr3:101398600-101402600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:101398600-101402800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:101398600-101403000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr3:101398600-101403800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:101398800-101400200	Strong transcription	Liver	Liver
43	chr3:101398800-101400400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr3:101398800-101400800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:101398800-101400800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:101398800-101400800	Strong transcription	Ovary	ovary
47	chr3:101398800-101401200	Strong transcription	Aorta	Aorta
48	chr3:101398800-101401400	Strong transcription	Gastric	stomach
49	chr3:101398800-101401400	Strong transcription	Lung	lung
50	chr3:101398800-101401400	Strong transcription	Thymus	Thymus

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