Variant report

Variant	rs7463083
Chromosome Location	chr8:54978127-54978128
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1039926	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs10504161	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs1050523	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs10958396	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10958397	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs11783652	0.82[CHB][hapmap]
rs11986577	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs11991952	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap]
rs11993959	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs11994629	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs12114043	0.85[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs12679542	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs16919699	0.80[CHB][hapmap]
rs16919782	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs16919784	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs2271567	0.87[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs2292590	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs4440612	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs4506187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4737479	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs4737487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs4737488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4738519	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6473911	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs6473914	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs6473915	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs7012031	0.93[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs7464767	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs7842911	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap]
rs9298497	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs952194	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023983	chr8:54790309-55145770	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539623	chr8:54790309-55145770	Bivalent Enhancer Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2758160	chr8:54832990-55016965	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759617	chr8:54832990-55016965	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv427821	chr8:54832990-55016965	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv1818072	chr8:54968014-54991447	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7463083	TCEA1	cis	lymphoblastoid	seeQTL
rs7463083	MRPL15	cis	cerebellum	SCAN
rs7463083	MRPL15	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54940200-54978200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr8:54944000-54985800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:54946400-54999200	Weak transcription	NHDF-Ad	bronchial
4	chr8:54949800-54999400	Weak transcription	NHLF	lung
5	chr8:54955200-54979000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr8:54955400-54978400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr8:54956000-54999000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr8:54956600-54991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr8:54957200-54991600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:54957600-54983400	Weak transcription	Stomach Mucosa	stomach
11	chr8:54957600-55009800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr8:54960000-54978600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr8:54960000-54993000	Weak transcription	Brain Substantia Nigra	brain
14	chr8:54960800-54978400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr8:54962200-54991000	Weak transcription	Esophagus	oesophagus
16	chr8:54963200-54983600	Weak transcription	Brain Angular Gyrus	brain
17	chr8:54963200-54999200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr8:54963200-54999200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr8:54963200-54999200	Weak transcription	Colonic Mucosa	Colon
20	chr8:54963200-54999200	Weak transcription	Small Intestine	intestine
21	chr8:54963400-54999200	Weak transcription	HSMMtube	muscle
22	chr8:54963800-54999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr8:54966200-54997600	Weak transcription	Pancreas	Pancrea
24	chr8:54966400-54979200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr8:54966400-54991800	Weak transcription	NH-A	brain
26	chr8:54966400-55007600	Weak transcription	Psoas Muscle	Psoas
27	chr8:54966400-55012800	Weak transcription	Fetal Kidney	kidney
28	chr8:54966600-54979200	Weak transcription	Fetal Brain Male	brain
29	chr8:54966600-54983000	Weak transcription	Brain Germinal Matrix	brain
30	chr8:54966600-54991800	Weak transcription	Osteobl	bone
31	chr8:54966600-55012800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr8:54967200-54983200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr8:54967200-54983400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr8:54967200-54991600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr8:54967200-54999200	Weak transcription	Ovary	ovary
36	chr8:54967600-54981000	Weak transcription	HSMM	muscle
37	chr8:54970200-54980000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr8:54970200-54981600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr8:54970400-54983400	Weak transcription	Fetal Lung	lung
40	chr8:54970400-54983600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr8:54971400-54978400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr8:54971400-54978400	Strong transcription	Dnd41	blood
43	chr8:54972000-54978400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr8:54972600-54978400	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr8:54973800-54978400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr8:54974200-54978400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr8:54974200-54978400	Strong transcription	NHEK	skin
48	chr8:54974400-54982200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr8:54974400-54985600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr8:54974400-54999200	Weak transcription	Rectal Mucosa Donor 31	rectum

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