Variant report

Variant	rs12809676
Chromosome Location	chr12:122442381-122442382
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122440790..122443569-chr12:122445704..122448468,2	MCF-7	breast:
2	chr12:122440832..122442485-chr12:122443851..122445815,2	K562	blood:
3	chr12:122237113..122238694-chr12:122441857..122444463,2	K562	blood:
4	chr12:122441336..122445469-chr12:122458589..122461636,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139725	Chromatin interaction
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10840630	1.00[ASN][1000 genomes]
rs10840631	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840632	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840633	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840637	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10840640	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10840641	0.82[AMR][1000 genomes]
rs11043225	1.00[ASN][1000 genomes]
rs11043233	1.00[ASN][1000 genomes]
rs11043244	1.00[ASN][1000 genomes]
rs11043246	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043251	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043271	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043278	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043280	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043288	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043294	0.84[AMR][1000 genomes]
rs1154514	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612028	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169070	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169071	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369331	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822775	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12823194	1.00[ASN][1000 genomes]
rs12824593	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825161	1.00[ASN][1000 genomes]
rs12827036	0.82[AMR][1000 genomes]
rs12830351	0.84[AMR][1000 genomes]
rs1720033	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720037	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167067	1.00[ASN][1000 genomes]
rs34159444	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906460	1.00[ASN][1000 genomes]
rs66751701	1.00[ASN][1000 genomes]
rs7132055	1.00[ASN][1000 genomes]
rs7298990	0.84[AMR][1000 genomes]
rs73217776	1.00[ASN][1000 genomes]
rs9739381	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12809676	BCL7A	cis	Muscle Skeletal	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122422800-122442600	Weak transcription	Fetal Kidney	kidney
2	chr12:122435200-122442400	Weak transcription	Pancreas	Pancrea
3	chr12:122438000-122444400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:122438600-122443600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr12:122439400-122443200	Enhancers	Brain Substantia Nigra	brain
6	chr12:122439800-122445200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:122440400-122443400	Enhancers	Brain Angular Gyrus	brain
8	chr12:122440400-122445800	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:122440600-122442600	Enhancers	Primary B cells from peripheral blood	blood
10	chr12:122440600-122443000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr12:122440600-122443400	Enhancers	Brain Hippocampus Middle	brain
12	chr12:122440800-122443400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr12:122440800-122445000	Weak transcription	Brain Germinal Matrix	brain
14	chr12:122441000-122442600	Enhancers	Primary B cells from cord blood	blood
15	chr12:122441000-122443400	Enhancers	Fetal Stomach	stomach
16	chr12:122441000-122445600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:122441200-122442600	Weak transcription	Brain Anterior Caudate	brain
18	chr12:122441200-122443000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:122441400-122442600	Enhancers	NH-A	brain
20	chr12:122441400-122443000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:122441400-122443000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:122441400-122443200	Enhancers	NHLF	lung
23	chr12:122441600-122442400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:122441600-122442400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:122441600-122443000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:122441600-122443000	Enhancers	NHDF-Ad	bronchial
27	chr12:122441600-122443400	Enhancers	Fetal Heart	heart
28	chr12:122441600-122443400	Enhancers	Fetal Muscle Leg	muscle
29	chr12:122441600-122443600	Enhancers	Spleen	Spleen
30	chr12:122441600-122443600	Flanking Active TSS	Dnd41	blood
31	chr12:122441600-122444000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr12:122441600-122444200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:122441600-122444800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:122441600-122444800	Flanking Active TSS	Fetal Thymus	thymus
35	chr12:122441600-122445800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr12:122441800-122442400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:122441800-122442800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:122441800-122442800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:122441800-122443000	Enhancers	Lung	lung
40	chr12:122441800-122443400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:122441800-122443400	Enhancers	Left Ventricle	heart
42	chr12:122441800-122443600	Flanking Active TSS	Thymus	Thymus
43	chr12:122441800-122444200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr12:122441800-122444200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:122441800-122444200	Enhancers	GM12878-XiMat	blood
46	chr12:122441800-122444400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr12:122441800-122444400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr12:122441800-122445800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:122441800-122445800	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr12:122442000-122442400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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