Variant report

Variant	rs3864012
Chromosome Location	chr3:101397623-101397624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:101397613-101398274	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:101397491-101398025	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr3:101397574-101399930	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:101395665-101400050	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr3:101395783-101401679	K562	blood:	n/a	n/a
6	POLR2A	chr3:101397621-101398297	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:101394844-101400076	K562	blood:	n/a	n/a
8	POLR2A	chr3:101397262-101398163	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr3:101394835-101398218	MCF-7	breast:	n/a	n/a
10	POLR2A	chr3:101397619-101398204	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:101397610-101398270	GM12891	blood:	n/a	n/a
12	POLR2A	chr3:101394709-101398094	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:101397534-101398118	U87	brain:	n/a	n/a
14	POLR2A	chr3:101394548-101402463	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:101397567-101400050	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:101397588-101398050	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:101394445-101400158	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr3:101394683-101399918	GM12892	blood:	n/a	n/a
19	POLR2A	chr3:101397560-101398269	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:101394828-101398273	GM12892	blood:	n/a	n/a
21	POLR2A	chr3:101397601-101398118	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr3:101397593-101398256	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:101397612-101398282	GM12891	blood:	n/a	n/a
24	POLR2A	chr3:101394775-101400361	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr3:101394763-101400062	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr3:101397333-101400882	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr3:101397554-101398160	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:101396566..101398165-chr3:101452263..101453813,2	MCF-7	breast:
2	chr3:101291104..101295547-chr3:101393750..101397705,12	MCF-7	breast:
3	chr3:101382560..101384971-chr3:101397220..101399534,3	MCF-7	breast:

No data

Variant related genes	Relation type
ZBTB11	TF binding region
ENSG00000081154	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1031710	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1056579	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1138818	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11706986	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11710533	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11710805	0.82[ASN][1000 genomes]
rs11711079	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11712748	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11714278	0.86[ASN][1000 genomes]
rs11717046	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11720745	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11914318	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11917569	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11917682	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11919389	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923273	0.80[AMR][1000 genomes]
rs11924013	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11925001	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12629658	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12629954	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12635128	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12636557	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12639028	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13059470	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13060963	0.81[ASN][1000 genomes]
rs13061565	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065944	0.80[ASN][1000 genomes]
rs13066768	0.86[ASN][1000 genomes]
rs13068350	0.81[ASN][1000 genomes]
rs13069443	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13077703	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13077925	0.86[ASN][1000 genomes]
rs13081846	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13082236	0.83[EUR][1000 genomes]
rs13099674	0.86[ASN][1000 genomes]
rs13100262	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17411983	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1963961	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1963962	0.86[ASN][1000 genomes]
rs2288272	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303474	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2318090	0.86[ASN][1000 genomes]
rs3094295	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094296	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094297	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3109756	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34181125	0.86[ASN][1000 genomes]
rs34301719	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34376498	0.86[ASN][1000 genomes]
rs34624546	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34883763	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35117343	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35850993	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36002990	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36060163	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3806653	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806654	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55654108	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55821257	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55859364	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56291106	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59596156	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62282218	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62284162	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62284198	0.86[ASN][1000 genomes]
rs62284199	0.86[ASN][1000 genomes]
rs71625262	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7629753	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7645391	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7651406	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7651721	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9830943	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

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
rs3864012	NXPE3	cis	Esophagus Muscularis	GTEx
rs3864012	RP11-49I4.3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101396000-101398800	Weak transcription	Aorta	Aorta
2	chr3:101396000-101398800	Weak transcription	Ovary	ovary
3	chr3:101396000-101399400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:101396200-101399400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:101396400-101399400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:101396400-101401200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:101396400-101402800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:101396600-101399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:101396800-101398600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:101396800-101398800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:101396800-101398800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:101397000-101398400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:101397000-101398400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:101397000-101398400	Weak transcription	Fetal Brain Female	brain
15	chr3:101397000-101398600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:101397000-101398600	Weak transcription	Fetal Lung	lung
17	chr3:101397000-101398800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:101397000-101398800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:101397000-101398800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:101397000-101398800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:101397000-101398800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:101397000-101399000	Weak transcription	Primary T cells from cord blood	blood
23	chr3:101397000-101399000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:101397000-101399000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:101397000-101399200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:101397000-101399200	Weak transcription	NHDF-Ad	bronchial
27	chr3:101397000-101399400	Weak transcription	Colonic Mucosa	Colon
28	chr3:101397000-101400000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:101397000-101400400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:101397000-101400400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:101397000-101402400	Weak transcription	Fetal Brain Male	brain
32	chr3:101397000-101402600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:101397200-101397800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:101397200-101398400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:101397200-101398400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:101397200-101398400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:101397200-101398600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr3:101397200-101398600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:101397200-101398600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:101397200-101398600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:101397200-101398600	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:101397200-101398600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:101397200-101398800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:101397200-101398800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:101397200-101398800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:101397200-101398800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:101397200-101398800	Weak transcription	Adipose Nuclei	Adipose
48	chr3:101397200-101398800	Weak transcription	Brain Angular Gyrus	brain
49	chr3:101397200-101398800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:101397200-101398800	Weak transcription	Brain Germinal Matrix	brain

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