Variant report

Variant	rs1863062
Chromosome Location	chr2:86517803-86517804
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10451631	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451666	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451668	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105865	1.00[CEU][hapmap]
rs11127018	0.81[JPT][hapmap]
rs17027263	1.00[CEU][hapmap]
rs28527367	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35807694	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35943273	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3731815	0.90[JPT][hapmap]
rs3731816	0.90[JPT][hapmap]
rs3821015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3827551	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs56657747	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56742104	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57006782	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57137376	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57279476	0.85[EUR][1000 genomes]
rs57412282	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57743711	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57786125	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57924251	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58029983	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58141172	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58210919	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58287226	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58728311	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58996019	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59149450	0.88[ASN][1000 genomes]
rs59300790	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59409236	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59523869	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59567456	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59697218	0.82[ASN][1000 genomes]
rs60032974	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60067772	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60237707	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60295664	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60345058	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60427833	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60474859	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60484746	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60791163	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60840060	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61392096	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61636758	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61669204	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61700819	1.00[EUR][1000 genomes]
rs6547685	1.00[CEU][hapmap]
rs6716825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748079	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6751871	1.00[CEU][hapmap]
rs6755760	1.00[CEU][hapmap]
rs6760222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72938375	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72940115	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940124	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940126	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940131	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940149	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940152	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940160	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753918	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606682	1.00[CEU][hapmap]

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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1863062	POLR1A	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86508000-86520200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:86508200-86519800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:86508600-86518400	Weak transcription	Fetal Brain Male	brain
4	chr2:86511000-86518000	Weak transcription	Fetal Kidney	kidney
5	chr2:86511200-86524000	Weak transcription	Aorta	Aorta
6	chr2:86512000-86518200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:86512000-86521800	Weak transcription	Fetal Intestine Small	intestine
8	chr2:86512400-86518000	Weak transcription	Brain Germinal Matrix	brain
9	chr2:86512400-86519600	Weak transcription	Fetal Brain Female	brain
10	chr2:86512400-86524000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:86513400-86520200	Weak transcription	Brain Anterior Caudate	brain
12	chr2:86514000-86529200	Weak transcription	Pancreas	Pancrea
13	chr2:86517200-86519000	Enhancers	Fetal Muscle Leg	muscle
14	chr2:86517400-86518200	Enhancers	Placenta	Placenta
15	chr2:86517400-86518200	Enhancers	Right Ventricle	heart
16	chr2:86517400-86521200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:86517400-86521200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:86517600-86518200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:86517600-86518400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:86517600-86518400	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:86517600-86518400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:86517600-86518800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:86517600-86519200	Enhancers	Left Ventricle	heart
24	chr2:86517600-86520600	Enhancers	Psoas Muscle	Psoas
25	chr2:86517600-86522000	Enhancers	Stomach Smooth Muscle	stomach
26	chr2:86517800-86518000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:86517800-86518000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:86517800-86518200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:86517800-86518200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:86517800-86518400	Enhancers	Adipose Nuclei	Adipose
31	chr2:86517800-86518800	Enhancers	HSMMtube	muscle
32	chr2:86517800-86519200	Enhancers	Colon Smooth Muscle	Colon
33	chr2:86517800-86524000	Weak transcription	Right Atrium	heart

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