Variant report

Variant	rs2293039
Chromosome Location	chr12:31454266-31454267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:31453530-31454668	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:31453558-31454599	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:31454244-31454534	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:31453562-31454916	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:31453620-31454648	K562	blood:	n/a	n/a
6	POLR2A	chr12:31453940-31454342	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:31453555-31454596	A549	lung:	n/a	n/a
8	POLR2A	chr12:31452583-31458592	K562	blood:	n/a	n/a
9	POLR2A	chr12:31453938-31454560	K562	blood:	n/a	n/a
10	POLR2A	chr12:31453387-31454708	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:31454232-31454318	K562	blood:	n/a	n/a
12	POLR2A	chr12:31453719-31454578	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:31453022..31454953-chr12:31477543..31481718,3	K562	blood:
2	chr12:31452762..31457432-chr12:31476482..31479243,5	MCF-7	breast:
3	chr12:31452911..31456081-chr12:31461692..31465766,4	K562	blood:
4	chr12:31447793..31455081-chr12:31455286..31461328,11	K562	blood:
5	chr12:31449988..31452418-chr12:31453015..31455328,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238661	TF binding region
FAM60A	TF binding region
ENSG00000139146	Chromatin interaction
ENSG00000256176	Chromatin interaction
ENSG00000238661	Chromatin interaction
ENSG00000177340	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10843918	1.00[EUR][1000 genomes]
rs11051394	1.00[EUR][1000 genomes]
rs11051395	1.00[EUR][1000 genomes]
rs11051396	1.00[EUR][1000 genomes]
rs11051399	1.00[EUR][1000 genomes]
rs11051402	1.00[EUR][1000 genomes]
rs11051403	1.00[EUR][1000 genomes]
rs11051409	1.00[EUR][1000 genomes]
rs12226982	1.00[EUR][1000 genomes]
rs12228674	1.00[EUR][1000 genomes]
rs12581740	1.00[EUR][1000 genomes]
rs17576073	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17576094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17576143	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17576150	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs17603871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17603906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17603947	0.81[CHB][hapmap]
rs2293040	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782688	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930974	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs57061710	1.00[EUR][1000 genomes]
rs60022875	1.00[EUR][1000 genomes]
rs7301494	1.00[EUR][1000 genomes]
rs9971805	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2758303	chr12:31125467-31491104	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	esv2759890	chr12:31125467-31491104	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv428276	chr12:31125467-31491104	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	esv2751043	chr12:31148662-31499671	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1045497	chr12:31213735-31458547	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	esv2751053	chr12:31225710-31484881	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	esv2754121	chr12:31225710-31493435	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	esv2751054	chr12:31225710-31513718	Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	esv35092	chr12:31239600-31484833	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
13	esv2751071	chr12:31239600-31493435	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
14	esv2751072	chr12:31239600-31499671	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
15	nsv430477	chr12:31239600-31513718	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
16	esv2751077	chr12:31278031-31499671	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
17	nsv524737	chr12:31399901-31464663	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers 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

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31426000-31460200	Weak transcription	Aorta	Aorta
2	chr12:31427200-31459800	Weak transcription	Gastric	stomach
3	chr12:31427600-31460800	Strong transcription	Fetal Thymus	thymus
4	chr12:31428600-31458600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:31428600-31470000	Weak transcription	Small Intestine	intestine
6	chr12:31430600-31462200	Weak transcription	Psoas Muscle	Psoas
7	chr12:31430800-31460600	Weak transcription	Right Ventricle	heart
8	chr12:31433000-31470200	Weak transcription	Stomach Mucosa	stomach
9	chr12:31434000-31456200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:31434600-31459800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:31435600-31458200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:31435600-31460600	Strong transcription	Dnd41	blood
13	chr12:31436200-31455400	Weak transcription	Fetal Brain Male	brain
14	chr12:31438400-31459600	Strong transcription	Hela-S3	cervix
15	chr12:31440200-31457600	Weak transcription	Brain Germinal Matrix	brain
16	chr12:31440200-31460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:31440400-31462200	Weak transcription	Osteobl	bone
18	chr12:31440800-31470000	Weak transcription	Fetal Lung	lung
19	chr12:31441200-31455400	Weak transcription	Ovary	ovary
20	chr12:31444000-31458400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:31445400-31460000	Weak transcription	Left Ventricle	heart
22	chr12:31445800-31459000	Strong transcription	K562	blood
23	chr12:31446200-31460400	Weak transcription	Brain Anterior Caudate	brain
24	chr12:31446600-31458200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:31446600-31468000	Weak transcription	Fetal Heart	heart
26	chr12:31446600-31470000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:31447800-31456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:31448000-31456200	Weak transcription	Adipose Nuclei	Adipose
29	chr12:31448000-31456200	Weak transcription	Fetal Brain Female	brain
30	chr12:31448000-31456400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:31448000-31457800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:31448000-31468000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:31448200-31455200	Weak transcription	Placenta	Placenta
34	chr12:31448200-31455400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:31448200-31456800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr12:31448400-31455400	Weak transcription	Fetal Kidney	kidney
37	chr12:31448400-31456600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:31448600-31461600	Weak transcription	NHLF	lung
39	chr12:31449000-31460800	Strong transcription	Primary T cells from cord blood	blood
40	chr12:31449400-31458200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:31449800-31457200	Weak transcription	Liver	Liver
42	chr12:31449800-31464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:31449800-31472800	Weak transcription	Pancreas	Pancrea
44	chr12:31450000-31455400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:31450000-31455600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:31450000-31455600	Weak transcription	HSMMtube	muscle
47	chr12:31450000-31456200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:31450000-31456200	Weak transcription	Lung	lung
49	chr12:31450000-31456200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:31450000-31464000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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