Variant report

Variant	rs6816010
Chromosome Location	chr4:48384499-48384500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10003230	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10026398	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10029785	0.89[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1055721	0.90[YRI][hapmap]
rs10805168	0.89[ASN][1000 genomes]
rs10938534	0.81[JPT][hapmap]
rs1117010	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11945562	0.86[JPT][hapmap]
rs12503644	0.85[ASN][1000 genomes]
rs12507206	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511991	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12645501	0.81[JPT][hapmap]
rs12645951	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[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]
rs12649527	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649528	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13105385	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13115295	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13133788	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13148849	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13150017	0.86[EUR][1000 genomes]
rs1352433	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1352434	0.88[ASN][1000 genomes]
rs1472967	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507865	0.81[JPT][hapmap]
rs1586540	0.92[ASN][1000 genomes]
rs1703973	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17575720	0.81[JPT][hapmap]
rs17656094	0.81[JPT][hapmap]
rs1948167	0.92[ASN][1000 genomes]
rs2029348	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291474	0.87[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353312	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353314	0.88[ASN][1000 genomes]
rs2353315	0.82[ASN][1000 genomes]
rs28409655	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34975258	0.82[ASN][1000 genomes]
rs35758434	0.92[ASN][1000 genomes]
rs372825	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs382335	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3828496	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs392187	0.83[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs404348	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404445	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs404656	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs411261	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs421336	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs421833	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs429969	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs432927	0.84[EUR][1000 genomes]
rs445892	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs449376	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs450498	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4536901	0.81[JPT][hapmap]
rs4694895	0.92[ASN][1000 genomes]
rs4695391	0.81[JPT][hapmap]
rs62309425	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447634	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447635	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811148	0.81[JPT][hapmap]
rs6816352	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6821277	0.87[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6829705	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6829716	0.86[JPT][hapmap]
rs6836010	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836632	0.86[JPT][hapmap]
rs6837335	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6844211	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848073	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848395	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7438704	0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7654770	0.86[JPT][hapmap]
rs7664981	0.94[YRI][hapmap]
rs7668529	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7672892	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7674269	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7678164	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678379	0.86[JPT][hapmap]
rs7679210	0.81[JPT][hapmap]
rs7683398	0.81[JPT][hapmap]
rs7693461	0.81[JPT][hapmap]
rs7697851	0.86[JPT][hapmap]
rs7700018	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs923372	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs923373	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9291323	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs937888	0.81[JPT][hapmap]
rs952289	0.81[JPT][hapmap]
rs974014	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs974015	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs974016	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs992423	0.86[JPT][hapmap]
rs9996532	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6816010	OCIAD2	cis	cerebellum	SCAN
rs6816010	SLAIN2	cis	parietal	SCAN
rs6816010	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
2	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:48357200-48384600	Weak transcription	Lung	lung
4	chr4:48361000-48384600	Weak transcription	Fetal Stomach	stomach
5	chr4:48362600-48384600	Weak transcription	Left Ventricle	heart
6	chr4:48363000-48384600	Weak transcription	Ovary	ovary
7	chr4:48363400-48405400	Weak transcription	Right Ventricle	heart
8	chr4:48368600-48384600	Weak transcription	Thymus	Thymus
9	chr4:48368800-48384600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:48371400-48395400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:48372600-48387000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
13	chr4:48372800-48384600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:48373000-48384800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:48374000-48384600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:48374000-48385600	Weak transcription	Right Atrium	heart
17	chr4:48375800-48384600	Weak transcription	K562	blood
18	chr4:48377800-48384600	Weak transcription	Pancreas	Pancrea
19	chr4:48377800-48405000	Weak transcription	Esophagus	oesophagus
20	chr4:48377800-48423800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:48378000-48384600	Weak transcription	Fetal Kidney	kidney
22	chr4:48378000-48384800	Weak transcription	Colonic Mucosa	Colon
23	chr4:48378000-48386400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:48378000-48390000	Weak transcription	NHLF	lung
25	chr4:48378000-48423800	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:48378200-48384600	Weak transcription	NHDF-Ad	bronchial
27	chr4:48378200-48386400	Weak transcription	Hela-S3	cervix
28	chr4:48378200-48398400	Weak transcription	A549	lung
29	chr4:48378400-48384600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:48378400-48384600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:48378400-48384600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr4:48378400-48384600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:48378400-48387000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:48378400-48395200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:48378400-48405000	Weak transcription	Gastric	stomach
36	chr4:48378400-48405200	Weak transcription	Psoas Muscle	Psoas
37	chr4:48378600-48384600	Weak transcription	Liver	Liver
38	chr4:48378600-48384600	Weak transcription	Fetal Intestine Small	intestine
39	chr4:48378600-48384600	Weak transcription	Osteobl	bone
40	chr4:48378600-48384800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:48378600-48395200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:48379000-48387200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:48379600-48391800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:48379600-48393600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:48379600-48400200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:48379800-48388200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:48380000-48389200	Strong transcription	Fetal Lung	lung
48	chr4:48380000-48392000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:48380000-48399200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr4:48380200-48387600	Strong transcription	Rectal Mucosa Donor 31	rectum

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