Variant report

Variant	rs1905108
Chromosome Location	chr8:49545585-49545586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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]
rs12545638	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]
rs12549320	0.91[CHB][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1976023	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2004389	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28770570	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56383226	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs745487	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs7463127	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1905108	EFCAB1	cis	cerebellum	SCAN
rs1905108	CUX2	trans	cerebellum	SCAN
rs1905108	EFCAB1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49534400-49556000	Weak transcription	Pancreas	Pancrea
2	chr8:49537600-49547000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr8:49538400-49545800	Weak transcription	Fetal Stomach	stomach
4	chr8:49538600-49546200	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:49539000-49546000	Weak transcription	Fetal Kidney	kidney
6	chr8:49540400-49545800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr8:49543200-49546000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr8:49543200-49546000	Weak transcription	Placenta	Placenta
9	chr8:49543200-49548000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:49543200-49548400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr8:49543400-49548000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr8:49543600-49548200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr8:49544200-49545800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr8:49544200-49545800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr8:49544200-49548200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:49544400-49545800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:49544400-49555400	Weak transcription	Osteobl	bone

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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