Variant report

Variant	rs12545638
Chromosome Location	chr8:49542850-49542851
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:49539159..49543167-chr8:49831897..49834584,3	MCF-7	breast:
2	chr8:49541767..49544762-chr8:49827612..49829547,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000019549	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12544004	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12549320	0.91[CHB][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1905108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1976023	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2004389	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28770570	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56383226	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745487	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs7463127	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12545638	EFCAB1	cis	parietal	SCAN
rs12545638	CUX2	trans	cerebellum	SCAN
rs12545638	EFCAB1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49534400-49556000	Weak transcription	Pancreas	Pancrea
2	chr8:49534600-49543000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:49537600-49547000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr8:49538400-49545800	Weak transcription	Fetal Stomach	stomach
5	chr8:49538600-49546200	Weak transcription	Fetal Muscle Leg	muscle
6	chr8:49538800-49544000	Enhancers	HMEC	breast
7	chr8:49539000-49543200	Enhancers	A549	lung
8	chr8:49539000-49543600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:49539000-49546000	Weak transcription	Fetal Kidney	kidney
10	chr8:49539200-49544200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr8:49539200-49544200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:49539600-49544000	Enhancers	NHEK	skin
13	chr8:49539800-49544200	Enhancers	NH-A	brain
14	chr8:49540000-49543000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr8:49540000-49543600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr8:49540200-49543000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr8:49540400-49543000	Weak transcription	NHLF	lung
18	chr8:49540400-49543200	Enhancers	Hela-S3	cervix
19	chr8:49540400-49545800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr8:49541600-49543000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr8:49541800-49543000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:49542200-49543200	Enhancers	Placenta	Placenta
23	chr8:49542200-49544000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr8:49542400-49543200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr8:49542400-49544000	Enhancers	HSMM	muscle
26	chr8:49542600-49543200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:49542600-49544400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr8:49542800-49543000	Enhancers	HUVEC	blood vessel
29	chr8:49542800-49543200	Enhancers	Spleen	Spleen
30	chr8:49542800-49543400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr8:49542800-49544200	Enhancers	NHDF-Ad	bronchial
32	chr8:49542800-49544400	Enhancers	Osteobl	bone

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