Variant report

Variant	rs4765914
Chromosome Location	chr12:2420377-2420378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:2419786..2421936-chr12:2425968..2427531,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1006737	0.81[MEX][hapmap]
rs1024582	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs10744560	0.81[MEX][hapmap]
rs10774035	0.81[MEX][hapmap]
rs10774037	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4298967	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap]
rs4765913	0.93[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4765914	EFCAB4B	cis	cerebellum	SCAN
rs4765914	CACNA1C	cis	parietal	SCAN
rs4765914	CACNA1C	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2406600-2420600	Weak transcription	Brain Germinal Matrix	brain
2	chr12:2416400-2420600	Weak transcription	Right Atrium	heart
3	chr12:2416400-2421000	Weak transcription	Fetal Heart	heart
4	chr12:2416400-2421200	Weak transcription	Aorta	Aorta
5	chr12:2416800-2423600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:2416800-2442200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:2417200-2424400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:2417200-2428400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:2418000-2421600	Enhancers	Rectal Smooth Muscle	rectum
10	chr12:2418000-2445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:2418800-2422600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:2419000-2420400	Enhancers	Colon Smooth Muscle	Colon
13	chr12:2419000-2420400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr12:2419000-2420400	Enhancers	NHLF	lung
15	chr12:2419000-2420800	Enhancers	Fetal Stomach	stomach
16	chr12:2419600-2420800	Enhancers	Osteobl	bone
17	chr12:2419600-2421000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:2419600-2421000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:2419600-2421800	Enhancers	Fetal Lung	lung
20	chr12:2419800-2420800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:2419800-2420800	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr12:2419800-2420800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr12:2419800-2420800	Enhancers	NH-A	brain
24	chr12:2419800-2420800	Flanking Active TSS	NHDF-Ad	bronchial
25	chr12:2420000-2420400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:2420000-2420400	Enhancers	Ovary	ovary
27	chr12:2420000-2420800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:2420000-2420800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:2420000-2420800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:2420000-2420800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:2420000-2420800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:2420000-2421000	Enhancers	Left Ventricle	heart
33	chr12:2420200-2420400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:2420200-2420400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:2420200-2420600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:2420200-2420800	Enhancers	Placenta	Placenta
37	chr12:2420200-2421600	Enhancers	Lung	lung

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