Variant report

Variant	rs12520759
Chromosome Location	chr5:42843771-42843772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1035516	0.87[AMR][1000 genomes]
rs1046068	0.86[JPT][hapmap]
rs10941592	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs10941593	0.82[CEU][hapmap]
rs11952526	0.84[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes]
rs11953554	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11958761	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12187996	0.86[JPT][hapmap]
rs12516954	0.80[AMR][1000 genomes]
rs12517112	0.86[JPT][hapmap]
rs12519443	0.83[AMR][1000 genomes]
rs12519532	0.82[CEU][hapmap]
rs12521615	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs12522458	0.89[AMR][1000 genomes]
rs13178745	0.81[AMR][1000 genomes]
rs1423649	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1423651	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423652	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2113086	0.82[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes]
rs2161600	0.89[AMR][1000 genomes]
rs28919892	0.86[JPT][hapmap];0.91[MEX][hapmap]
rs34417548	0.82[ASN][1000 genomes]
rs35896631	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3797310	0.86[JPT][hapmap]
rs3849695	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4866799	0.87[AMR][1000 genomes]
rs4866803	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4866804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4866805	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4866806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4866949	0.89[JPT][hapmap]
rs4866966	0.83[AMR][1000 genomes]
rs4866967	0.90[AMR][1000 genomes]
rs55687632	0.90[AMR][1000 genomes]
rs55688895	0.90[AMR][1000 genomes]
rs58394380	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59073137	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60008560	0.83[AMR][1000 genomes]
rs61099053	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61371942	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62370951	0.87[AMR][1000 genomes]
rs62370953	0.87[AMR][1000 genomes]
rs62370959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6865453	0.82[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs6880056	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6882786	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6896902	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7579	0.86[JPT][hapmap];0.91[MEX][hapmap]
rs7703376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7708223	0.86[JPT][hapmap]
rs7719242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7725776	0.85[JPT][hapmap]
rs7725961	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs7730190	0.86[JPT][hapmap]
rs7734918	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs7735857	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs882775	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9687651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
6	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
7	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
8	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
11	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
12	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
13	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12520759	OXCT1	cis	parietal	SCAN
rs12520759	SEPP1	Cis_1M	lymphoblastoid	RTeQTL
rs12520759	CCDC152	cis	Artery Aorta	GTEx
rs12520759	CCDC152	cis	Artery Tibial	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42840800-42843800	Enhancers	HepG2	liver
2	chr5:42840800-42844200	Enhancers	Adipose Nuclei	Adipose
3	chr5:42841200-42844400	Enhancers	Liver	Liver
4	chr5:42841600-42844000	Weak transcription	Ovary	ovary
5	chr5:42842800-42844000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr5:42842800-42844000	Enhancers	Osteobl	bone
7	chr5:42842800-42844200	Enhancers	HSMMtube	muscle
8	chr5:42843000-42843800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:42843000-42844200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:42843200-42843800	Enhancers	Brain Angular Gyrus	brain
11	chr5:42843200-42843800	Flanking Active TSS	Fetal Heart	heart
12	chr5:42843200-42843800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr5:42843200-42843800	Enhancers	K562	blood
14	chr5:42843200-42844000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:42843200-42844000	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr5:42843200-42844000	Enhancers	Psoas Muscle	Psoas
17	chr5:42843200-42844200	Enhancers	Rectal Smooth Muscle	rectum
18	chr5:42843400-42844000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:42843400-42844000	Enhancers	Left Ventricle	heart
20	chr5:42843400-42844200	Enhancers	Fetal Intestine Large	intestine
21	chr5:42843400-42844200	Enhancers	Fetal Lung	lung
22	chr5:42843400-42845200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:42843600-42843800	Weak transcription	Brain Substantia Nigra	brain
24	chr5:42843600-42844200	Enhancers	Brain Anterior Caudate	brain
25	chr5:42843600-42844200	Enhancers	HSMM	muscle
26	chr5:42843600-42844400	Enhancers	Fetal Intestine Small	intestine

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