Variant report

Variant	rs12189001
Chromosome Location	chr5:60680244-60680245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10041978	0.86[ASN][1000 genomes]
rs1045352	0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10939900	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939901	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939902	0.99[ASN][1000 genomes]
rs10939903	0.86[ASN][1000 genomes]
rs10939905	0.80[ASN][1000 genomes]
rs11742658	0.80[ASN][1000 genomes]
rs11743711	0.88[ASN][1000 genomes]
rs11747564	0.80[ASN][1000 genomes]
rs11749200	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11750589	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11950318	0.84[ASN][1000 genomes]
rs11952146	0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11954430	0.82[ASN][1000 genomes]
rs12187112	0.94[ASN][1000 genomes]
rs12188627	0.93[ASN][1000 genomes]
rs12518479	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522647	0.86[ASN][1000 genomes]
rs13156100	0.80[ASN][1000 genomes]
rs13157657	0.82[ASN][1000 genomes]
rs13157831	0.80[ASN][1000 genomes]
rs13158675	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160801	0.82[ASN][1000 genomes]
rs13162358	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163970	0.82[ASN][1000 genomes]
rs13169711	1.00[ASN][1000 genomes]
rs13170135	0.98[ASN][1000 genomes]
rs13170262	0.82[ASN][1000 genomes]
rs13171497	0.80[ASN][1000 genomes]
rs13171757	0.88[ASN][1000 genomes]
rs13172080	0.82[ASN][1000 genomes]
rs13172084	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs13178686	0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179091	0.80[ASN][1000 genomes]
rs13181015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185068	0.80[ASN][1000 genomes]
rs13186194	0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs13188327	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13188685	0.80[ASN][1000 genomes]
rs1348716	0.82[ASN][1000 genomes]
rs1374043	0.82[ASN][1000 genomes]
rs1445976	0.80[ASN][1000 genomes]
rs1445979	0.86[ASN][1000 genomes]
rs1445980	0.80[ASN][1000 genomes]
rs1445981	0.80[ASN][1000 genomes]
rs1477355	0.86[ASN][1000 genomes]
rs1986252	0.82[ASN][1000 genomes]
rs2034239	0.80[ASN][1000 genomes]
rs2053693	0.80[ASN][1000 genomes]
rs2053694	0.80[ASN][1000 genomes]
rs2276987	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs28610339	0.99[ASN][1000 genomes]
rs34739794	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35262187	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4392578	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484384	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604142	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5027472	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55838118	0.80[ASN][1000 genomes]
rs56035042	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60529601	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60886975	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62368660	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449526	0.81[GIH][hapmap];0.91[MEX][hapmap]
rs6449527	0.81[CEU][hapmap];0.92[MEX][hapmap]
rs6449528	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6449529	1.00[ASN][1000 genomes]
rs6449530	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449531	0.99[ASN][1000 genomes]
rs6449532	0.99[ASN][1000 genomes]
rs6449533	0.99[ASN][1000 genomes]
rs6449535	0.86[ASN][1000 genomes]
rs66775554	0.80[ASN][1000 genomes]
rs6860608	0.93[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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6865624	0.80[ASN][1000 genomes]
rs6873712	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6874264	0.80[ASN][1000 genomes]
rs6877610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878927	0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs6879809	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6881765	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885005	0.99[ASN][1000 genomes]
rs6890351	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6894675	0.99[ASN][1000 genomes]
rs6895046	0.82[ASN][1000 genomes]
rs7443602	0.80[ASN][1000 genomes]
rs7700289	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701440	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7709645	0.99[ASN][1000 genomes]
rs7714457	0.82[ASN][1000 genomes]
rs7714712	0.99[ASN][1000 genomes]
rs7717082	0.82[ASN][1000 genomes]
rs7719647	0.82[ASN][1000 genomes]
rs7722810	0.87[ASN][1000 genomes]
rs7724551	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7727824	0.99[ASN][1000 genomes]
rs7734879	0.99[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	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12189001	ERCC8	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60653800-60681200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:60654000-60681400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:60658800-60686600	Weak transcription	Fetal Stomach	stomach
4	chr5:60659000-60681600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:60659000-60703800	Weak transcription	Primary B cells from cord blood	blood
6	chr5:60659200-60686600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr5:60659400-60703600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:60659600-60697600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:60660200-60681600	Weak transcription	HSMM	muscle
10	chr5:60661800-60686800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr5:60662200-60686800	Weak transcription	NHLF	lung
12	chr5:60663200-60686800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:60663400-60690000	Weak transcription	Psoas Muscle	Psoas
14	chr5:60665400-60686800	Weak transcription	Aorta	Aorta
15	chr5:60665600-60681600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:60667600-60681600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:60667800-60689800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:60667800-60689800	Weak transcription	NHEK	skin
19	chr5:60668600-60680800	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:60668600-60681400	Weak transcription	Fetal Intestine Small	intestine
21	chr5:60675000-60680800	Weak transcription	Spleen	Spleen
22	chr5:60675000-60681600	Weak transcription	Pancreas	Pancrea
23	chr5:60675000-60686800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:60675400-60692800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:60675600-60681200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:60675800-60681400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:60675800-60681400	Weak transcription	A549	lung
28	chr5:60675800-60692800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:60676400-60681200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:60676600-60681400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:60676600-60681600	Weak transcription	Esophagus	oesophagus
32	chr5:60677200-60681400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:60677400-60689400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:60677600-60681200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:60677600-60681200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:60677600-60681400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr5:60677600-60682000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:60678000-60681000	Weak transcription	Small Intestine	intestine
39	chr5:60678000-60681200	Weak transcription	Brain Angular Gyrus	brain
40	chr5:60678000-60681200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:60678000-60681200	Weak transcription	Brain Substantia Nigra	brain
42	chr5:60678200-60681200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:60679200-60686800	Weak transcription	Lung	lung
44	chr5:60679800-60681400	Weak transcription	Fetal Muscle Leg	muscle
45	chr5:60680200-60680400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:60680200-60680400	Enhancers	Brain Anterior Caudate	brain
47	chr5:60680200-60680400	Enhancers	HSMMtube	muscle

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