Variant report

Variant	rs900240
Chromosome Location	chr8:49555905-49555906
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	chr8:49554509..49556220-chr8:49558044..49560777,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10099531	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957178	0.89[EUR][1000 genomes]
rs10957179	0.89[EUR][1000 genomes]
rs10957183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12542549	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12544004	0.91[EUR][1000 genomes]
rs12545705	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1473441	0.85[TSI][hapmap]
rs1809451	0.89[AFR][1000 genomes]
rs2128241	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62509321	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62509354	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7831800	0.81[AMR][1000 genomes]
rs900239	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9650145	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9650146	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs900240	EFCAB1	cis	cerebellum	SCAN
rs900240	EFCAB1	cis	parietal	SCAN
rs900240	EFCAB1	cis	Skin Sun Exposed Lower leg	GTEx

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	chr8:49550400-49556000	Weak transcription	NH-A	brain
3	chr8:49551200-49560800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr8:49551200-49563400	Enhancers	Ovary	ovary
5	chr8:49552000-49556200	Weak transcription	Left Ventricle	heart
6	chr8:49553000-49560000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr8:49553400-49556800	Enhancers	Fetal Lung	lung
8	chr8:49553400-49556800	Enhancers	HSMMtube	muscle
9	chr8:49553600-49556200	Weak transcription	Right Atrium	heart
10	chr8:49554000-49556800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr8:49554200-49556800	Enhancers	Fetal Stomach	stomach
12	chr8:49554400-49557200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr8:49554600-49556800	Enhancers	Fetal Heart	heart
14	chr8:49554800-49556000	Weak transcription	Aorta	Aorta
15	chr8:49554800-49556200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr8:49555000-49556800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:49555000-49556800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr8:49555200-49556400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr8:49555200-49556800	Enhancers	Colon Smooth Muscle	Colon
20	chr8:49555200-49557000	Enhancers	Adipose Nuclei	Adipose
21	chr8:49555400-49556400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:49555400-49556600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr8:49555400-49556800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr8:49555400-49556800	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr8:49555400-49556800	Enhancers	Osteobl	bone
26	chr8:49555600-49556000	Weak transcription	Placenta	Placenta
27	chr8:49555600-49556600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr8:49555600-49556800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:49555600-49556800	Enhancers	NHLF	lung
30	chr8:49555800-49556200	Weak transcription	Fetal Kidney	kidney
31	chr8:49555800-49556600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr8:49555800-49557000	Enhancers	Fetal Muscle Leg	muscle

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