Variant report

Variant	rs12106834
Chromosome Location	chr3:142883975-142883976
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	FOXM1	chr3:142883366-142884738	GM12878	blood:	n/a	n/a
2	CEBPB	chr3:142883198-142884304	GM12878	blood:	n/a	n/a
3	MTA3	chr3:142883647-142884790	GM12878	blood:	n/a	n/a
4	EP300	chr3:142883656-142884327	GM12878	blood:	n/a	chr3:142884210-142884224
5	EBF1	chr3:142883705-142884895	GM12878	blood:	n/a	n/a
6	BCL3	chr3:142883521-142884049	GM12878	blood:	n/a	n/a
7	CUX1	chr3:142883755-142884163	GM12878	blood:	n/a	n/a
8	MEF2A	chr3:142883540-142884129	GM12878	blood:	n/a	chr3:142883828-142883843
9	STAT3	chr3:142883764-142884865	MCF10A-Er-Src	breast:	n/a	chr3:142884671-142884680 chr3:142883857-142883865 chr3:142884670-142884679
10	NFIC	chr3:142883432-142884308	GM12878	blood:	n/a	n/a
11	MTA3	chr3:142883117-142884823	GM12878	blood:	n/a	n/a
12	TBL1XR1	chr3:142883482-142884300	GM12878	blood:	n/a	n/a
13	RUNX3	chr3:142883535-142884792	GM12878	blood:	n/a	n/a
14	RUNX3	chr3:142883526-142884126	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:142883866-142884735	MCF10A-Er-Src	breast:	n/a	n/a
16	PML	chr3:142883689-142884020	GM12878	blood:	n/a	n/a
17	NFATC1	chr3:142883506-142884222	GM12878	blood:	n/a	n/a
18	NFATC1	chr3:142883495-142884159	GM12878	blood:	n/a	n/a
19	IKZF1	chr3:142883658-142884751	GM12878	blood:	n/a	n/a
20	STAT3	chr3:142883684-142884070	MCF10A-Er-Src	breast:	n/a	chr3:142883857-142883865
21	STAT3	chr3:142883764-142884420	GM12878	blood:	n/a	chr3:142883857-142883865
22	FOS	chr3:142883773-142884043	MCF10A-Er-Src	breast:	n/a	n/a
23	SMC3	chr3:142883736-142884175	GM12878	blood:	n/a	n/a
24	MEF2A	chr3:142883582-142884182	GM12878	blood:	n/a	chr3:142883828-142883843
25	RCOR1	chr3:142883366-142884478	GM12878	blood:	n/a	n/a
26	MEF2C	chr3:142883619-142884143	GM12878	blood:	n/a	chr3:142883828-142883843
27	ATF2	chr3:142883476-142884102	GM12878	blood:	n/a	n/a
28	BCLAF1	chr3:142883450-142884081	GM12878	blood:	n/a	n/a
29	ATF2	chr3:142883498-142884818	GM12878	blood:	n/a	n/a
30	FOS	chr3:142883767-142884038	MCF10A-Er-Src	breast:	n/a	n/a
31	BATF	chr3:142883652-142884050	GM12878	blood:	n/a	n/a
32	BATF	chr3:142883729-142884024	GM12878	blood:	n/a	n/a
33	ZNF143	chr3:142883753-142884156	GM12878	blood:	n/a	n/a
34	NFIC	chr3:142883215-142884946	GM12878	blood:	n/a	n/a
35	FOS	chr3:142883877-142884854	MCF10A-Er-Src	breast:	n/a	chr3:142884671-142884679 chr3:142884672-142884679 chr3:142884671-142884680
36	FOXM1	chr3:142883524-142884819	GM12878	blood:	n/a	n/a
37	BCL11A	chr3:142883668-142884076	GM12878	blood:	n/a	n/a
38	EP300	chr3:142883700-142884086	GM12878	blood:	n/a	n/a
39	STAT5A	chr3:142883625-142884033	GM12878	blood:	n/a	chr3:142883857-142883865
40	STAT3	chr3:142883764-142883975	MCF10A-Er-Src	breast:	n/a	chr3:142883857-142883865
41	IRF4	chr3:142883626-142884091	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142837036..142839934-chr3:142882781..142884331,2	K562	blood:

Variant related genes	Relation type
ENSG00000211483	TF binding region
ENSG00000175040	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12489438	0.82[AFR][1000 genomes]
rs72996485	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv508250	chr3:142842454-142943722	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv529013	chr3:142877227-142888043	Weak transcription Enhancers Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142877800-142884200	Weak transcription	Osteobl	bone
2	chr3:142877800-142886000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:142878200-142884200	Weak transcription	NHDF-Ad	bronchial
4	chr3:142879600-142886600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:142879800-142884000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:142881200-142888600	Enhancers	Primary T cells from cord blood	blood
7	chr3:142881800-142885200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr3:142882000-142884200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr3:142882000-142884800	Enhancers	Fetal Lung	lung
10	chr3:142882000-142885000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr3:142882000-142888400	Enhancers	Dnd41	blood
12	chr3:142882000-142891600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr3:142882200-142884400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:142882200-142884600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:142882200-142889000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:142882400-142885200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr3:142882400-142889600	Enhancers	Fetal Thymus	thymus
18	chr3:142882600-142884600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:142882600-142884600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:142882800-142884400	Enhancers	Placenta	Placenta
21	chr3:142882800-142884800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr3:142882800-142889200	Weak transcription	Fetal Stomach	stomach
23	chr3:142883000-142884000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:142883000-142884200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:142883000-142884200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:142883000-142884200	Weak transcription	K562	blood
27	chr3:142883000-142885200	Enhancers	Primary hematopoietic stem cells	blood
28	chr3:142883200-142884600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:142883400-142884200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:142883600-142884000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:142883600-142884000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:142883600-142884000	Enhancers	GM12878-XiMat	blood
33	chr3:142883600-142884600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:142883600-142884600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr3:142883600-142884600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:142883600-142887800	Weak transcription	Primary B cells from cord blood	blood
37	chr3:142883800-142884600	Enhancers	Adipose Nuclei	Adipose
38	chr3:142883800-142884600	Enhancers	Thymus	Thymus
39	chr3:142883800-142884600	Enhancers	NHLF	lung
40	chr3:142883800-142885400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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