Variant report

Variant	rs12542203
Chromosome Location	chr8:49705759-49705760
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:49694708..49697435-chr8:49704058..49706751,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10090157	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10090819	0.85[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap]
rs10092718	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10097910	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10101066	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10108023	0.80[ASN][1000 genomes]
rs10111821	0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs1126259	0.82[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11785748	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12155607	1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12547015	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12547603	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12547619	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12548278	0.94[JPT][hapmap]
rs12550270	0.88[ASN][1000 genomes]
rs13271216	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13276316	0.85[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap]
rs1482261	0.85[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs2384970	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2891648	0.85[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs35243529	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873084	0.83[EUR][1000 genomes]
rs4873285	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4873287	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4873288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873290	0.81[MEX][hapmap]
rs55923266	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6472038	0.81[ASN][1000 genomes]
rs6984858	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6990865	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7007780	0.81[MEX][hapmap]
rs7835152	0.87[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs900238	0.80[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs9298058	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs966703	0.82[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12542203	EFCAB1	cis	parietal	SCAN
rs12542203	C8orf22	cis	cerebellum	SCAN
rs12542203	EFCAB1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49703000-49716800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:49703800-49706000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:49704600-49705800	Weak transcription	Fetal Kidney	kidney
4	chr8:49704800-49705800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:49704800-49706000	Weak transcription	Fetal Lung	lung
6	chr8:49705600-49706000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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