Variant report

Variant	rs10089017
Chromosome Location	chr8:49566471-49566472
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	chr8:49565766..49568245-chr8:49569048..49571269,2	MCF-7	breast:

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]
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	0.84[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]
rs10107998	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]
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
rs10089017	EFCAB1	cis	cerebellum	SCAN
rs10089017	EFCAB1	cis	parietal	SCAN

Chromatin state (count:44 , 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	chr8:49563200-49566600	Weak transcription	Right Atrium	heart
7	chr8:49563200-49566600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr8:49563200-49572800	Weak transcription	Pancreas	Pancrea
9	chr8:49563800-49566800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr8:49563800-49567000	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr8:49563800-49567800	Enhancers	Ovary	ovary
12	chr8:49564000-49567400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:49564200-49566600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr8:49564400-49566800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr8:49564400-49571200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr8:49564800-49566600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr8:49564800-49567600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr8:49565000-49570200	Weak transcription	Aorta	Aorta
19	chr8:49565200-49566800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr8:49565400-49566600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr8:49565400-49566600	Enhancers	Fetal Thymus	thymus
22	chr8:49565400-49567400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:49565400-49567600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr8:49565400-49567600	Enhancers	Fetal Stomach	stomach
25	chr8:49565400-49567600	Enhancers	HSMM	muscle
26	chr8:49565400-49567600	Enhancers	HSMMtube	muscle
27	chr8:49565400-49567600	Enhancers	NHDF-Ad	bronchial
28	chr8:49565400-49567600	Enhancers	NHLF	lung
29	chr8:49565600-49566600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr8:49565600-49567600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:49565800-49566600	Weak transcription	Lung	lung
32	chr8:49565800-49568800	Weak transcription	Left Ventricle	heart
33	chr8:49566000-49566600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr8:49566000-49567000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr8:49566000-49568200	Enhancers	Fetal Lung	lung
36	chr8:49566200-49567200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr8:49566200-49567200	Enhancers	NH-A	brain
38	chr8:49566200-49567600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr8:49566200-49567600	Enhancers	Fetal Muscle Leg	muscle
40	chr8:49566400-49566600	Enhancers	Colon Smooth Muscle	Colon
41	chr8:49566400-49567000	Enhancers	Fetal Kidney	kidney
42	chr8:49566400-49567400	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr8:49566400-49567600	Enhancers	Placenta	Placenta
44	chr8:49566400-49567800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links