Variant report

Variant	rs12139364
Chromosome Location	chr1:45890155-45890156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10789463	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789465	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs10890328	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10890329	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10890331	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211109	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211122	0.89[ASN][1000 genomes]
rs11211129	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap]
rs11580609	0.95[CHB][hapmap]
rs12119202	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568144	0.87[ASN][1000 genomes]
rs12729715	0.87[ASN][1000 genomes]
rs12738318	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12739418	0.81[EUR][1000 genomes]
rs12743512	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.89[ASN][1000 genomes]
rs1417578	0.87[JPT][hapmap]
rs1765709	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1771551	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2036021	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2050884	0.87[JPT][hapmap]
rs2153607	0.87[JPT][hapmap]
rs2153608	0.87[JPT][hapmap]
rs2275276	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs2298018	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2356413	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2487442	0.87[JPT][hapmap]
rs2492840	0.87[JPT][hapmap]
rs2492841	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660851	0.87[JPT][hapmap]
rs4660853	0.83[JPT][hapmap]
rs4660854	0.87[JPT][hapmap]
rs4660859	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4660861	0.88[ASN][1000 genomes]
rs512026	0.95[CHB][hapmap]
rs518365	0.91[CHB][hapmap];0.83[MEX][hapmap]
rs6657237	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6661321	0.89[ASN][1000 genomes]
rs66732088	0.81[AFR][1000 genomes]
rs71500084	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7532762	0.87[JPT][hapmap]
rs781058	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs781226	0.83[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap]
rs781230	0.81[ASN][1000 genomes]
rs781232	0.83[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7903	0.95[CHB][hapmap]
rs937291	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs9429072	0.87[JPT][hapmap]
rs9429076	0.83[JPT][hapmap]
rs9429158	0.81[JPT][hapmap]
rs998199	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12139364	CCDC163P	cis	Esophagus Muscularis	GTEx
rs12139364	MUTYH	cis	multi-tissue	Pritchard
rs12139364	RIMKLA	cis	cerebellum	SCAN
rs12139364	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs12139364	CCDC163P	cis	Muscle Skeletal	GTEx
rs12139364	CCDC163P	cis	Artery Tibial	GTEx
rs12139364	Hs.396207	cis	multi-tissue	Pritchard
rs12139364	CCDC163P	cis	Thyroid	GTEx
rs12139364	CCDC163P	cis	lung	GTEx
rs12139364	CCDC163P	cis	Whole Blood	GTEx
rs12139364	FIG4	trans	parietal	SCAN
rs12139364	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs12139364	IPP	cis	lymphoblastoid	seeQTL
rs12139364	TESK2	cis	cerebellum	SCAN
rs12139364	CYP4Z2P	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45880200-45895600	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:45884600-45910600	Weak transcription	Ovary	ovary
3	chr1:45885400-45890200	Weak transcription	Left Ventricle	heart
4	chr1:45886800-45908200	Weak transcription	Fetal Intestine Small	intestine
5	chr1:45887200-45895400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:45887600-45909200	Weak transcription	Liver	Liver
7	chr1:45888000-45895600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:45888000-45910000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:45888200-45920600	Weak transcription	Primary B cells from cord blood	blood
10	chr1:45889000-45897400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:45889400-45890200	Enhancers	Fetal Stomach	stomach
12	chr1:45889600-45890200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:45889600-45890200	Enhancers	K562	blood
14	chr1:45889800-45890400	Enhancers	Brain Cingulate Gyrus	brain
15	chr1:45889800-45940600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:45890000-45890200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:45890000-45890200	Enhancers	Fetal Lung	lung
18	chr1:45890000-45890600	Enhancers	Brain Substantia Nigra	brain

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