Variant report

Variant	rs4957343
Chromosome Location	chr5:40695070-40695071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10035235	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs10035697	0.89[ASN][1000 genomes]
rs10038251	0.89[ASN][1000 genomes]
rs10038367	0.87[ASN][1000 genomes]
rs10042459	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10043839	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10043891	0.89[ASN][1000 genomes]
rs10044538	0.89[ASN][1000 genomes]
rs10053469	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10053664	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10056173	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10057182	0.89[ASN][1000 genomes]
rs10062565	0.83[JPT][hapmap]
rs10065482	0.89[ASN][1000 genomes]
rs10066459	0.85[ASW][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10068069	0.81[ASN][1000 genomes]
rs10069737	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10071870	0.89[ASN][1000 genomes]
rs10074117	0.89[AFR][1000 genomes]
rs1015027	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];0.96[MKK][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10473210	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10473211	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10473214	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10941522	0.89[ASN][1000 genomes]
rs10941525	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];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11744569	0.89[ASN][1000 genomes]
rs11747210	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs11949581	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12188666	0.87[ASN][1000 genomes]
rs12513529	0.89[ASN][1000 genomes]
rs12517210	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs12518018	0.81[ASN][1000 genomes]
rs12520058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12523329	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1363847	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1553578	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1553579	0.89[ASN][1000 genomes]
rs17835256	0.95[ASN][1000 genomes]
rs2194204	0.86[ASN][1000 genomes]
rs2270625	0.83[JPT][hapmap]
rs2291782	0.83[JPT][hapmap]
rs35693860	0.89[ASN][1000 genomes]
rs3792827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3805489	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3805490	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs3805492	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs3805494	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs3805498	0.80[ASN][1000 genomes]
rs3805499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3816959	0.83[JPT][hapmap]
rs4599576	0.85[ASN][1000 genomes]
rs4957334	1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs4957336	0.89[ASN][1000 genomes]
rs4957337	0.89[ASN][1000 genomes]
rs4957338	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4957339	0.89[ASN][1000 genomes]
rs4957347	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56752286	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62356460	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62356461	0.89[ASN][1000 genomes]
rs62356468	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62356508	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62358056	0.85[ASN][1000 genomes]
rs62358796	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62358800	0.87[ASN][1000 genomes]
rs6868112	0.89[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs6884507	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72747928	0.89[ASN][1000 genomes]
rs72747930	0.89[ASN][1000 genomes]
rs72747940	0.85[ASN][1000 genomes]
rs72747952	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72747958	0.86[ASN][1000 genomes]
rs7717814	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7719692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7721093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7725810	0.82[GIH][hapmap];0.83[JPT][hapmap]
rs9292784	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9292785	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4957343	OXCT1	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40684000-40700600	Weak transcription	Left Ventricle	heart
2	chr5:40684600-40700400	Weak transcription	Right Ventricle	heart
3	chr5:40688400-40696400	Weak transcription	Liver	Liver
4	chr5:40688400-40700400	Weak transcription	Stomach Mucosa	stomach
5	chr5:40688800-40696800	Weak transcription	Fetal Lung	lung
6	chr5:40688800-40697000	Strong transcription	Fetal Thymus	thymus
7	chr5:40688800-40718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:40690000-40695800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:40690200-40695200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:40690400-40695200	Strong transcription	HSMM	muscle
11	chr5:40690400-40697200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:40690600-40695400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr5:40690800-40695800	Weak transcription	A549	lung
14	chr5:40691200-40695200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr5:40691200-40697000	Strong transcription	Primary T cells from cord blood	blood
16	chr5:40691600-40695200	Strong transcription	Adipose Nuclei	Adipose
17	chr5:40691600-40695400	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr5:40692200-40701800	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:40692400-40695200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:40692600-40698600	Weak transcription	HSMMtube	muscle
22	chr5:40692800-40695200	Strong transcription	Dnd41	blood
23	chr5:40692800-40700400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:40692800-40700400	Weak transcription	Esophagus	oesophagus
25	chr5:40692800-40700400	Weak transcription	Gastric	stomach
26	chr5:40692800-40700400	Weak transcription	Pancreas	Pancrea
27	chr5:40692800-40700400	Weak transcription	Small Intestine	intestine
28	chr5:40692800-40700600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr5:40692800-40702400	Weak transcription	Colonic Mucosa	Colon
30	chr5:40692800-40721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:40692800-40733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:40692800-40735000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:40693000-40698200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:40693000-40700800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:40693000-40701800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:40693000-40701800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:40693000-40702000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:40693000-40702000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:40693600-40696600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:40693600-40727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:40693800-40695400	Weak transcription	NH-A	brain
42	chr5:40693800-40700000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr5:40694200-40695800	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr5:40694400-40695200	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr5:40694400-40699000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:40694600-40695600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:40694600-40695800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:40694600-40698400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:40694600-40700400	Weak transcription	Lung	lung
50	chr5:40694600-40700600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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