Variant report

Variant	rs3109756
Chromosome Location	chr3:101398919-101398920
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:101398324-101399801	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:101397879-101399883	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:101398657-101399871	K562	blood:	n/a	n/a
4	POLR2A	chr3:101398386-101400417	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:101398385-101399947	U87	brain:	n/a	n/a
6	POLR2A	chr3:101398318-101399231	MCF-7	breast:	n/a	n/a
7	POLR2A	chr3:101398577-101399004	ProgFib	skin:	n/a	n/a
8	ATF2	chr3:101398890-101399886	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:101398330-101399853	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:101398311-101399851	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:101397574-101399930	Hela-S3	cervix:	n/a	n/a
12	CHD2	chr3:101398864-101399498	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:101398301-101401459	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:101398329-101399871	U87	brain:	n/a	n/a
15	POLR2A	chr3:101395665-101400050	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr3:101395783-101401679	K562	blood:	n/a	n/a
17	POLR2A	chr3:101398328-101399843	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:101398473-101399308	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:101398298-101399889	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:101398299-101399775	K562	blood:	n/a	n/a
21	POLR2A	chr3:101397708-101399866	HepG2	liver:	n/a	n/a
22	PML	chr3:101398712-101399631	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:101398417-101399818	A549	lung:	n/a	n/a
24	POLR2A	chr3:101394844-101400076	K562	blood:	n/a	n/a
25	POLR2A	chr3:101398391-101401007	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:101398199-101400566	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr3:101398298-101400096	GM12891	blood:	n/a	n/a
28	POLR2A	chr3:101398704-101399834	K562	blood:	n/a	n/a
29	POLR2A	chr3:101398871-101399905	U87	brain:	n/a	n/a
30	POLR2A	chr3:101394548-101402463	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr3:101398340-101399807	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr3:101397567-101400050	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:101398398-101398923	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr3:101398557-101399787	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:101398409-101401956	K562	blood:	n/a	n/a
36	POLR2A	chr3:101398431-101399778	K562	blood:	n/a	n/a
37	POLR2A	chr3:101398560-101399783	K562	blood:	n/a	n/a
38	POLR2A	chr3:101398355-101399854	U87	brain:	n/a	n/a
39	POLR2A	chr3:101394445-101400158	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr3:101394683-101399918	GM12892	blood:	n/a	n/a
41	POLR2A	chr3:101398310-101399725	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr3:101398333-101399823	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr3:101398648-101399170	K562	blood:	n/a	n/a
44	POLR2A	chr3:101398846-101399869	IMR90	lung:	n/a	n/a
45	POLR2A	chr3:101398039-101399781	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr3:101398398-101398985	HepG2	liver:	n/a	n/a
47	POLR2A	chr3:101398708-101399164	HCT-116	colon:	n/a	n/a
48	POLR2A	chr3:101398382-101400948	GM12891	blood:	n/a	n/a
49	POLR2A	chr3:101398833-101399113	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr3:101398760-101399734	HCT-116	colon:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:101382560..101384971-chr3:101397220..101399534,3	MCF-7	breast:
2	chr3:101390217..101392058-chr3:101398423..101400158,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZBTB11	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1031710	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1056579	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1138818	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11706986	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11710533	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11710805	0.85[ASN][1000 genomes]
rs11711079	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11712748	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714278	0.86[ASN][1000 genomes]
rs11717046	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11720745	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11914318	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11917569	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11917682	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11919389	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923273	0.81[AMR][1000 genomes]
rs11924013	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11925001	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629658	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12629954	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12635128	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12636557	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12639028	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13059470	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13060963	0.87[ASN][1000 genomes]
rs13061565	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13065944	0.86[ASN][1000 genomes]
rs13066768	0.89[ASN][1000 genomes]
rs13068350	0.81[ASN][1000 genomes]
rs13069443	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13077703	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077925	0.89[ASN][1000 genomes]
rs13081846	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13082236	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13084432	0.80[ASN][1000 genomes]
rs13096323	0.83[ASN][1000 genomes]
rs13099674	0.89[ASN][1000 genomes]
rs13100262	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17411983	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1963961	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1963962	0.89[ASN][1000 genomes]
rs2288272	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303474	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2318090	0.89[ASN][1000 genomes]
rs3094295	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3094296	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3094297	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34181125	0.89[ASN][1000 genomes]
rs34301719	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34376498	0.89[ASN][1000 genomes]
rs34624546	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34883763	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35117343	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35850993	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36002990	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36060163	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806653	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806654	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3864012	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55654108	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55821257	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55859364	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56291106	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59596156	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62282218	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62284162	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62284198	0.89[ASN][1000 genomes]
rs62284199	0.89[ASN][1000 genomes]
rs71625262	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7629753	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7645391	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651406	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7651721	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9830943	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[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
rs3109756	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs3109756	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	chr3:101396000-101399400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:101396200-101399400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:101396400-101399400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:101396400-101401200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:101396400-101402800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:101396600-101399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:101397000-101399000	Weak transcription	Primary T cells from cord blood	blood
8	chr3:101397000-101399000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:101397000-101399000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:101397000-101399200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:101397000-101399200	Weak transcription	NHDF-Ad	bronchial
12	chr3:101397000-101399400	Weak transcription	Colonic Mucosa	Colon
13	chr3:101397000-101400000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:101397000-101400400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:101397000-101400400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:101397000-101402400	Weak transcription	Fetal Brain Male	brain
17	chr3:101397000-101402600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:101397200-101399000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:101397200-101399000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:101397200-101399000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:101397200-101399000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:101397200-101399000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:101397200-101399000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:101397200-101399000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:101397200-101399000	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:101397200-101399000	Weak transcription	Fetal Kidney	kidney
27	chr3:101397200-101399000	Weak transcription	Psoas Muscle	Psoas
28	chr3:101397200-101399000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:101397200-101399000	Weak transcription	GM12878-XiMat	blood
30	chr3:101397200-101399000	Weak transcription	HSMM	muscle
31	chr3:101397200-101399000	Weak transcription	NHEK	skin
32	chr3:101397200-101399200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:101397200-101399200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:101397200-101399200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:101397200-101399200	Weak transcription	NH-A	brain
36	chr3:101397200-101399400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:101397200-101399400	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:101397200-101400800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:101397200-101402600	Weak transcription	Right Atrium	heart
40	chr3:101397200-101402600	Weak transcription	Right Ventricle	heart
41	chr3:101397200-101402800	Weak transcription	Fetal Heart	heart
42	chr3:101397400-101399000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:101397400-101399000	Weak transcription	Brain Anterior Caudate	brain
44	chr3:101397400-101399000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:101397400-101399000	Weak transcription	Pancreas	Pancrea
46	chr3:101397400-101399000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:101397400-101399000	Weak transcription	NHLF	lung
48	chr3:101397400-101399200	Weak transcription	Stomach Mucosa	stomach
49	chr3:101397400-101399200	Weak transcription	Osteobl	bone
50	chr3:101397400-101399400	Weak transcription	Primary B cells from cord blood	blood

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