Variant report

Variant	rs1377059
Chromosome Location	chr4:82272961-82272962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:82263937..82264497-chr4:82272498..82273225,2	K562	blood:
2	chr4:82005126..82005787-chr4:82272560..82273161,2	MCF-7	breast:
3	chr4:81990998..81991602-chr4:82272501..82273357,5	MCF-7	breast:
4	chr4:81990848..81991586-chr4:82272501..82273236,3	K562	blood:
5	chr4:81990624..81991565-chr4:82272517..82273470,4	MCF-7	breast:
6	chr4:82005004..82005857-chr4:82272588..82273446,6	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10013788	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10017744	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10021462	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028610	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11727754	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11731567	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11732090	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732106	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11733845	0.91[EUR][1000 genomes]
rs11736471	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11736583	0.89[AMR][1000 genomes]
rs11939135	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11942269	0.91[EUR][1000 genomes]
rs12332030	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13435660	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1443542	0.84[EUR][1000 genomes]
rs1452364	0.91[EUR][1000 genomes]
rs1452366	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1551236	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17428097	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17428153	0.89[AMR][1000 genomes]
rs17499131	0.91[EUR][1000 genomes]
rs17500037	0.89[AMR][1000 genomes]
rs17500100	0.88[AMR][1000 genomes]
rs1993160	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2034630	0.92[EUR][1000 genomes]
rs2041461	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2058367	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4693234	0.95[EUR][1000 genomes]
rs62303573	0.86[EUR][1000 genomes]
rs6535243	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6814785	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6819909	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6821450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6831114	0.91[EUR][1000 genomes]
rs6839968	0.84[CEU][hapmap]
rs6853731	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7654102	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7660089	0.89[AMR][1000 genomes]
rs7664953	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7669131	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7673578	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7677239	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7680637	0.94[EUR][1000 genomes]
rs7685645	0.95[EUR][1000 genomes]
rs7694769	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9307782	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829985	chr4:82199328-82353656	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1377059	PRKG2	cis	Nerve Tibial	GTEx
rs1377059	C4orf11	cis	cerebellum	SCAN
rs1377059	PAQR3	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82267600-82273400	Enhancers	Fetal Intestine Large	intestine
2	chr4:82270200-82273000	Weak transcription	Fetal Lung	lung
3	chr4:82271000-82273000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:82271000-82273000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:82271000-82273800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:82271400-82273400	Enhancers	Fetal Intestine Small	intestine
7	chr4:82272000-82274200	Enhancers	NHLF	lung
8	chr4:82272200-82275400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:82272400-82273000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:82272400-82273000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:82272400-82273000	Enhancers	Stomach Mucosa	stomach
12	chr4:82272400-82273200	Enhancers	NHDF-Ad	bronchial
13	chr4:82272400-82273600	Enhancers	Fetal Kidney	kidney
14	chr4:82272800-82273000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:82272800-82273200	Enhancers	Fetal Brain Male	brain

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