Variant report

Variant	rs34889961
Chromosome Location	chr3:112247331-112247332
allele	C/T
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	chr3:112247074-112248291	K562	blood:	n/a	n/a

Variant related genes	Relation type
OR7E100P	TF binding region

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10511317	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1072896	1.00[AFR][1000 genomes]
rs11919639	0.89[EUR][1000 genomes]
rs11921669	0.89[EUR][1000 genomes]
rs12630906	1.00[AFR][1000 genomes]
rs12634199	1.00[AFR][1000 genomes]
rs12637057	1.00[AFR][1000 genomes]
rs12637953	1.00[AFR][1000 genomes]
rs13059364	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13063173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064534	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065703	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070342	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071492	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078401	1.00[AFR][1000 genomes]
rs13079599	1.00[AFR][1000 genomes]
rs13080547	0.92[EUR][1000 genomes]
rs13080749	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13081201	0.92[EUR][1000 genomes]
rs13081265	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13081632	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13086960	1.00[AFR][1000 genomes]
rs13088339	0.92[EUR][1000 genomes]
rs13088349	0.92[EUR][1000 genomes]
rs13088467	0.92[EUR][1000 genomes]
rs13092057	0.85[EUR][1000 genomes]
rs13094161	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13094649	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095000	0.92[EUR][1000 genomes]
rs13096943	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs16845067	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16845068	1.00[AFR][1000 genomes]
rs16845073	1.00[AFR][1000 genomes]
rs16859661	0.96[EUR][1000 genomes]
rs16859674	0.89[EUR][1000 genomes]
rs16859727	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859775	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16859779	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16859787	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859793	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859849	1.00[AFR][1000 genomes]
rs16859890	1.00[AFR][1000 genomes]
rs16859897	1.00[AFR][1000 genomes]
rs16859930	1.00[AFR][1000 genomes]
rs16859961	1.00[AFR][1000 genomes]
rs2220656	0.92[EUR][1000 genomes]
rs2705526	0.92[EUR][1000 genomes]
rs28364588	1.00[AFR][1000 genomes]
rs28364589	1.00[AFR][1000 genomes]
rs28365853	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34080815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139211	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34248586	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34284082	0.89[EUR][1000 genomes]
rs34541731	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34596334	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34597203	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34645913	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34829517	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34949685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34962178	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35107041	0.89[EUR][1000 genomes]
rs35240469	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255669	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35263368	1.00[AFR][1000 genomes]
rs35349986	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35512450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35526995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35529363	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35692417	0.92[EUR][1000 genomes]
rs35709173	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35725070	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35748518	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35803911	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35840933	0.92[EUR][1000 genomes]
rs35931975	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs36025914	0.92[EUR][1000 genomes]
rs36031379	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36045008	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs36061184	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36146261	0.92[EUR][1000 genomes]
rs36153507	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3736269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736270	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736271	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773698	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773701	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773704	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773706	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773710	0.92[EUR][1000 genomes]
rs3821684	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55742760	0.92[EUR][1000 genomes]
rs56662636	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56856838	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56952692	1.00[AFR][1000 genomes]
rs56970524	0.92[EUR][1000 genomes]
rs57224143	1.00[AFR][1000 genomes]
rs57346109	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58657519	1.00[AFR][1000 genomes]
rs58891772	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59191788	1.00[AFR][1000 genomes]
rs59279185	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59650289	1.00[AFR][1000 genomes]
rs59858117	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60112764	1.00[AFR][1000 genomes]
rs60321074	0.92[EUR][1000 genomes]
rs60340975	1.00[AFR][1000 genomes]
rs60646325	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60733172	1.00[AFR][1000 genomes]
rs66486470	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66546764	1.00[AFR][1000 genomes]
rs66698345	0.89[EUR][1000 genomes]
rs66791711	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs66910014	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67021100	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67204151	0.92[EUR][1000 genomes]
rs67513863	0.89[EUR][1000 genomes]
rs67940544	0.92[EUR][1000 genomes]
rs67944354	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71317505	0.92[EUR][1000 genomes]
rs71317506	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71317507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71317508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71317510	0.92[EUR][1000 genomes]
rs724125	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229398	0.92[EUR][1000 genomes]
rs958935	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963541	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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	39 gene(s)	inside rSNPs	diseases
8	nsv965197	chr3:112238965-112250194	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
2	chr3:112234000-112247600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:112237200-112247400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:112237200-112254200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:112238200-112247400	Weak transcription	GM12878-XiMat	blood
7	chr3:112238600-112249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:112239800-112247400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:112239800-112247800	Weak transcription	Aorta	Aorta
11	chr3:112239800-112247800	Weak transcription	Esophagus	oesophagus
12	chr3:112241000-112251600	Weak transcription	HUVEC	blood vessel
13	chr3:112241600-112259400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:112242000-112247400	Weak transcription	Spleen	Spleen
15	chr3:112242000-112247800	Weak transcription	Gastric	stomach
16	chr3:112242000-112248400	Weak transcription	NHDF-Ad	bronchial
17	chr3:112242200-112247400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:112242200-112247600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:112242200-112248000	Weak transcription	Fetal Intestine Small	intestine
20	chr3:112242200-112252200	Weak transcription	NHLF	lung
21	chr3:112242400-112247800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:112242400-112247800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:112242400-112249800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:112242600-112263800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:112243000-112271600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:112243400-112247400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:112244000-112247400	Weak transcription	Brain Anterior Caudate	brain
28	chr3:112244000-112259800	Weak transcription	Pancreas	Pancrea
29	chr3:112244200-112247400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:112244200-112247600	Weak transcription	Fetal Lung	lung
31	chr3:112244200-112251200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:112244400-112247400	Weak transcription	Colonic Mucosa	Colon
33	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
34	chr3:112244400-112278200	Weak transcription	K562	blood
35	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
36	chr3:112244600-112256200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:112244600-112264800	Weak transcription	NHEK	skin
38	chr3:112245000-112249600	Strong transcription	Liver	Liver
39	chr3:112245000-112249800	Strong transcription	Adipose Nuclei	Adipose
40	chr3:112245200-112263200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:112245200-112273200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:112245400-112248200	Strong transcription	Fetal Brain Female	brain
43	chr3:112245400-112248400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:112245400-112248600	Strong transcription	Primary B cells from cord blood	blood
45	chr3:112245400-112262800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:112245600-112247800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:112245600-112248000	Strong transcription	Osteobl	bone
48	chr3:112245600-112249600	Strong transcription	Brain Hippocampus Middle	brain
49	chr3:112245600-112249800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:112245600-112249800	Strong transcription	Placenta	Placenta

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