Variant report

Variant	rs6716825
Chromosome Location	chr2:86538070-86538071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:149222241..149225264-chr2:86537194..86540871,3	MCF-7	breast:
2	chr2:86536580..86540172-chr2:86541032..86544003,3	K562	blood:

Variant related genes	Relation type
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10451631	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451665	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451666	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451668	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127018	0.81[JPT][hapmap]
rs17027263	1.00[CEU][hapmap]
rs1863062	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]
rs28527367	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35807694	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35943273	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];1.00[CHD][hapmap]
rs56657747	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56742104	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57006782	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57137376	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	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57786125	0.93[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	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	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59149450	0.88[ASN][1000 genomes]
rs59300790	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59409236	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59523869	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59567456	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59697218	0.82[ASN][1000 genomes]
rs60032974	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	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60345058	0.93[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	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60791163	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60840060	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	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61700819	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6728494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748079	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6760222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72938375	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72940115	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940124	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940126	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940131	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72940149	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940152	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940160	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753918	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593666	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6716825	POLR1A	cis	lymphoblastoid	seeQTL
rs6716825	POLR1A	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86525800-86540800	Weak transcription	Aorta	Aorta
2	chr2:86529400-86539200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:86533000-86538600	Weak transcription	Fetal Brain Female	brain
4	chr2:86533000-86542800	Weak transcription	Fetal Intestine Small	intestine
5	chr2:86533200-86563000	Weak transcription	Brain Germinal Matrix	brain
6	chr2:86534600-86538200	Enhancers	Fetal Heart	heart
7	chr2:86535200-86539600	Enhancers	Rectal Smooth Muscle	rectum
8	chr2:86535800-86539600	Enhancers	Colon Smooth Muscle	Colon
9	chr2:86535800-86539600	Enhancers	Fetal Stomach	stomach
10	chr2:86536200-86559800	Weak transcription	HSMMtube	muscle
11	chr2:86536600-86539200	Enhancers	Stomach Smooth Muscle	stomach
12	chr2:86536800-86538200	Weak transcription	Psoas Muscle	Psoas
13	chr2:86536800-86540200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:86536800-86542200	Weak transcription	Right Atrium	heart
15	chr2:86537200-86538200	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:86537200-86541200	Weak transcription	Right Ventricle	heart
17	chr2:86537200-86541400	Weak transcription	Left Ventricle	heart
18	chr2:86537600-86540800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:86537600-86563000	Weak transcription	Brain Anterior Caudate	brain
20	chr2:86537800-86538800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:86538000-86538200	Enhancers	Fetal Lung	lung
22	chr2:86538000-86538400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr2:86538000-86538600	Enhancers	Skeletal Muscle Male	skeletal muscle

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