Variant report

Variant	rs1563396
Chromosome Location	chr8:121359701-121359702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10096828	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1031576	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955969	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11774731	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11776868	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11782639	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13255609	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13438950	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563391	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563392	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1563393	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563394	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563395	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563397	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563398	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563399	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2034843	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2034844	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168406	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168407	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2198750	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290521	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290523	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290524	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34104524	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35248031	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4143484	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4870726	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4871058	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4871059	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4871060	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6469917	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6469918	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6982921	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6987036	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7001798	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7003062	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7017523	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7821701	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7823806	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7823977	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7824821	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7828515	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7828729	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7832817	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7838078	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7846160	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs930852	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650079	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9650080	0.88[ASN][1000 genomes]
rs980825	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891420	chr8:121194900-121561369	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv612112	chr8:121234298-121385167	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv891421	chr8:121292407-121653902	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1563396	MRPL13	cis	cerebellum	SCAN
rs1563396	NOV	cis	parietal	SCAN
rs1563396	MTBP	cis	cerebellum	SCAN
rs1563396	MTBP	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121320400-121372600	Weak transcription	Fetal Intestine Small	intestine
2	chr8:121333800-121383800	Weak transcription	Fetal Intestine Large	intestine
3	chr8:121344200-121361400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr8:121346400-121377600	Weak transcription	Colon Smooth Muscle	Colon
5	chr8:121354000-121360000	Enhancers	HSMM	muscle
6	chr8:121354400-121361400	Strong transcription	Fetal Lung	lung
7	chr8:121355400-121359800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:121356200-121360200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr8:121356200-121360200	Enhancers	NHDF-Ad	bronchial
10	chr8:121356200-121360400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr8:121356600-121360200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr8:121357200-121359800	Strong transcription	Ovary	ovary
13	chr8:121357200-121360000	Enhancers	Osteobl	bone
14	chr8:121358000-121372000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr8:121358400-121359800	Enhancers	HUVEC	blood vessel
16	chr8:121358400-121360000	Enhancers	HMEC	breast
17	chr8:121358600-121360200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:121358800-121359800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr8:121358800-121359800	Genic enhancers	Aorta	Aorta
20	chr8:121358800-121359800	Enhancers	NHEK	skin
21	chr8:121358800-121360000	Enhancers	HSMMtube	muscle
22	chr8:121358800-121360000	Enhancers	NH-A	brain
23	chr8:121358800-121360200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr8:121358800-121360200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr8:121358800-121360200	Strong transcription	Placenta	Placenta
26	chr8:121359000-121359800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr8:121359000-121359800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr8:121359000-121359800	Enhancers	Fetal Brain Male	brain
29	chr8:121359000-121359800	Enhancers	Fetal Muscle Leg	muscle
30	chr8:121359000-121359800	Enhancers	NHLF	lung
31	chr8:121359200-121359800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr8:121359200-121359800	Genic enhancers	Fetal Stomach	stomach
33	chr8:121359600-121359800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr8:121359600-121359800	Enhancers	Esophagus	oesophagus
35	chr8:121359600-121359800	Enhancers	Rectal Smooth Muscle	rectum
36	chr8:121359600-121360000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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