Variant report

Variant	rs6728494
Chromosome Location	chr2:86532989-86532990
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86530903..86533565-chr2:86534462..86536704,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10451631	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451665	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451666	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451668	0.85[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];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28527367	0.85[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]
rs56657747	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56742104	0.85[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	0.85[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	0.85[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	0.85[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	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61700819	1.00[EUR][1000 genomes]
rs6716825	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[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[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	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940152	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940160	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753918	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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
rs6728494	POLR1A	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86524200-86533600	Enhancers	Fetal Lung	lung
2	chr2:86524600-86533400	Enhancers	Fetal Muscle Leg	muscle
3	chr2:86525800-86540800	Weak transcription	Aorta	Aorta
4	chr2:86529400-86535600	Weak transcription	Psoas Muscle	Psoas
5	chr2:86529400-86535600	Weak transcription	Right Ventricle	heart
6	chr2:86529400-86539200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:86529600-86534600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:86529600-86535600	Weak transcription	Right Atrium	heart
9	chr2:86529800-86537200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:86530000-86537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:86530200-86535800	Weak transcription	HSMMtube	muscle
12	chr2:86531200-86533200	Enhancers	Brain Germinal Matrix	brain
13	chr2:86531600-86533200	Enhancers	Rectal Smooth Muscle	rectum
14	chr2:86532000-86533400	Enhancers	Colon Smooth Muscle	Colon
15	chr2:86532400-86533000	Bivalent Enhancer	Fetal Stomach	stomach
16	chr2:86532400-86533000	Enhancers	Left Ventricle	heart
17	chr2:86532600-86533000	Enhancers	Fetal Intestine Small	intestine
18	chr2:86532600-86534600	Weak transcription	Fetal Heart	heart
19	chr2:86532800-86533000	Enhancers	Fetal Brain Female	brain
20	chr2:86532800-86533200	Enhancers	Fetal Muscle Trunk	muscle
21	chr2:86532800-86535200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:86532800-86535600	Weak transcription	Stomach Smooth Muscle	stomach

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