Variant report

Variant	rs12309291
Chromosome Location	chr12:58293664-58293665
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	RUNX3	chr12:58292084-58293685	GM12878	blood:	n/a	chr12:58293361-58293370 chr12:58293361-58293370
2	STAT3	chr12:58292296-58293686	GM12878	blood:	n/a	chr12:58293210-58293218 chr12:58292527-58292534 chr12:58292794-58292801 chr12:58293174-58293186
3	GATA3	chr12:58292583-58293728	SK-N-SH	brain:	n/a	chr12:58292989-58292999
4	NFIC	chr12:58292026-58293669	GM12878	blood:	n/a	n/a
5	BHLHE40	chr12:58292259-58293717	GM12878	blood:	n/a	n/a
6	TBP	chr12:58292530-58293740	GM12878	blood:	n/a	n/a
7	EBF1	chr12:58292372-58293684	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58257612..58259236-chr12:58293224..58296608,3	MCF-7	breast:
2	chr12:58238331..58240066-chr12:58291999..58293854,2	K562	blood:
3	chr12:58225758..58227356-chr12:58293010..58294775,2	MCF-7	breast:
4	chr12:58236711..58242486-chr12:58286970..58293951,15	MCF-7	breast:
5	chr12:58289871..58291670-chr12:58291918..58293741,2	K562	blood:

Variant related genes	Relation type
ENSG00000245651	TF binding region
ENSG00000245651	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11172376	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172377	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834260	1.00[ASN][1000 genomes]
rs12296922	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12322495	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12322586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119981	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17119991	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34241380	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34372362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35441007	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35985500	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61935768	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137226	1.00[GIH][hapmap]
rs7977734	1.00[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58290200-58293800	Flanking Active TSS	GM12878-XiMat	blood
2	chr12:58290600-58293800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr12:58290600-58293800	Enhancers	HMEC	breast
4	chr12:58290800-58293800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:58290800-58294200	Enhancers	Primary B cells from cord blood	blood
6	chr12:58290800-58294200	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:58290800-58294200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:58291000-58294000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:58291000-58294000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:58291000-58294000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr12:58291000-58294200	Enhancers	Fetal Thymus	thymus
12	chr12:58291000-58294400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:58291000-58294400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr12:58291200-58293800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:58291200-58293800	Enhancers	Primary T cells from cord blood	blood
16	chr12:58291200-58294000	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:58291200-58294000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr12:58291200-58294200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:58291400-58293800	Enhancers	Duodenum Mucosa	Duodenum
20	chr12:58291600-58293800	Enhancers	Thymus	Thymus
21	chr12:58291600-58294000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:58292000-58293800	Bivalent Enhancer	Dnd41	blood
23	chr12:58292400-58293800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr12:58292600-58294000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:58292800-58298800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:58292800-58299000	Weak transcription	Fetal Kidney	kidney
27	chr12:58292800-58299000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:58293200-58293800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:58293200-58293800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr12:58293200-58294000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr12:58293200-58294400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:58293200-58295800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:58293200-58295800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:58293200-58295800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:58293200-58296000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:58293200-58296000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:58293200-58296200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:58293200-58296600	Weak transcription	Pancreas	Pancrea
39	chr12:58293200-58298000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:58293200-58298800	Weak transcription	Adipose Nuclei	Adipose
41	chr12:58293200-58298800	Weak transcription	Placenta	Placenta
42	chr12:58293200-58299000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:58293200-58299000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:58293200-58299000	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:58293200-58299000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:58293200-58299000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:58293200-58299000	Weak transcription	Brain Substantia Nigra	brain
48	chr12:58293200-58299000	Weak transcription	Fetal Lung	lung
49	chr12:58293200-58299000	Weak transcription	A549	lung
50	chr12:58293200-58299000	Weak transcription	NHDF-Ad	bronchial

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