Variant report

Variant	rs10107998
Chromosome Location	chr8:49566969-49566970
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	chr8:49565766..49568245-chr8:49569048..49571269,2	MCF-7	breast:
2	chr8:49566599..49568855-chr8:49570957..49573457,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253892	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10086031	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10086847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10089017	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10094884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10097910	0.85[CEU][hapmap]
rs10098811	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10429408	0.85[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes]
rs10504066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11992055	0.85[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs11994273	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12549717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13248205	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13251674	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13257444	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13275840	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13278011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13439150	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1482264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16938259	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16938260	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16938290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16938363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2046236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2170491	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28496614	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs33997479	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34036465	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35116039	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35306055	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35379802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35545096	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35564937	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36071901	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4873281	1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4873282	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4873283	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4873284	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6988001	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6989273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71511941	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745488	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs966703	0.82[ASW][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10107998	EFCAB1	cis	cerebellum	SCAN
rs10107998	EFCAB1	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49560600-49567600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr8:49561000-49567600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr8:49561000-49567600	Enhancers	Osteobl	bone
4	chr8:49561400-49567000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr8:49563000-49569400	Weak transcription	Spleen	Spleen
6	chr8:49563200-49572800	Weak transcription	Pancreas	Pancrea
7	chr8:49563800-49567000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr8:49563800-49567800	Enhancers	Ovary	ovary
9	chr8:49564000-49567400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr8:49564400-49571200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr8:49564800-49567600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:49565000-49570200	Weak transcription	Aorta	Aorta
13	chr8:49565400-49567400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:49565400-49567600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:49565400-49567600	Enhancers	Fetal Stomach	stomach
16	chr8:49565400-49567600	Enhancers	HSMM	muscle
17	chr8:49565400-49567600	Enhancers	HSMMtube	muscle
18	chr8:49565400-49567600	Enhancers	NHDF-Ad	bronchial
19	chr8:49565400-49567600	Enhancers	NHLF	lung
20	chr8:49565600-49567600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr8:49565800-49568800	Weak transcription	Left Ventricle	heart
22	chr8:49566000-49567000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:49566000-49568200	Enhancers	Fetal Lung	lung
24	chr8:49566200-49567200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr8:49566200-49567200	Enhancers	NH-A	brain
26	chr8:49566200-49567600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:49566200-49567600	Enhancers	Fetal Muscle Leg	muscle
28	chr8:49566400-49567000	Enhancers	Fetal Kidney	kidney
29	chr8:49566400-49567400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr8:49566400-49567600	Enhancers	Placenta	Placenta
31	chr8:49566400-49567800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr8:49566600-49567600	Enhancers	Fetal Intestine Small	intestine
33	chr8:49566600-49567600	Enhancers	Fetal Muscle Trunk	muscle
34	chr8:49566600-49567600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr8:49566600-49568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr8:49566800-49567000	Enhancers	Small Intestine	intestine
37	chr8:49566800-49567200	Weak transcription	Lung	lung
38	chr8:49566800-49568400	Weak transcription	Primary monocytes fromperipheralblood	blood

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