Variant report

Variant	rs12548278
Chromosome Location	chr8:49695775-49695776
allele	A/G
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:
2	chr8:49692576..49695901-chr8:49698756..49701661,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10090819	0.83[JPT][hapmap]
rs10097910	0.83[JPT][hapmap]
rs10101066	0.89[JPT][hapmap]
rs10108023	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10111821	0.83[JPT][hapmap]
rs1074382	0.80[JPT][hapmap]
rs10808720	0.80[JPT][hapmap]
rs1126259	0.89[JPT][hapmap]
rs13251991	0.80[JPT][hapmap]
rs13276316	0.88[JPT][hapmap]
rs1482261	0.83[ASW][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap]
rs1482262	0.82[ASW][hapmap];0.80[JPT][hapmap]
rs16938731	0.84[ASN][1000 genomes]
rs1871889	0.86[CEU][hapmap];0.80[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2891648	0.83[ASW][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap]
rs3750259	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs4873285	0.89[JPT][hapmap]
rs4873286	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4873288	0.89[JPT][hapmap]
rs4873289	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6415598	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6472038	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6472050	0.84[AMR][1000 genomes]
rs6984858	0.83[JPT][hapmap]
rs6990865	0.83[JPT][hapmap]
rs900237	0.82[ASW][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap]
rs900238	0.89[JPT][hapmap]
rs9298058	0.89[JPT][hapmap]
rs966703	0.89[JPT][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12548278	EFCAB1	cis	Esophagus Mucosa	GTEx
rs12548278	EFCAB1	cis	cerebellum	SCAN
rs12548278	EFCAB1	cis	Esophagus Muscularis	GTEx
rs12548278	EFCAB1	cis	parietal	SCAN
rs12548278	EFCAB1	cis	Nerve Tibial	GTEx
rs12548278	EFCAB1	cis	Skin Sun Exposed Lower leg	GTEx
rs12548278	EFCAB1	cis	brain	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49677600-49700200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:49686600-49700400	Weak transcription	Esophagus	oesophagus
3	chr8:49690600-49701200	Weak transcription	Ovary	ovary
4	chr8:49691000-49700400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:49691200-49705400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:49691400-49699800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:49691600-49699200	Weak transcription	Fetal Lung	lung
8	chr8:49693400-49698800	Weak transcription	Adipose Nuclei	Adipose
9	chr8:49693400-49699000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr8:49693800-49701200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr8:49694400-49700200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr8:49694800-49700400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:49694800-49700400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr8:49695400-49696200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:49695400-49696400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr8:49695400-49697600	Weak transcription	Fetal Brain Male	brain
17	chr8:49695600-49696000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr8:49695600-49696000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:49695600-49696000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr8:49695600-49696200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr8:49695600-49696400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr8:49695600-49696400	Enhancers	Fetal Kidney	kidney

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