Variant report

Variant	rs12595728
Chromosome Location	chr15:56266789-56266790
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	chr15:56260979..56263208-chr15:56266401..56268573,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11071234	0.94[ASN][1000 genomes]
rs11632096	0.86[EUR][1000 genomes]
rs11632295	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11636123	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11637576	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595359	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1509406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2089635	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2089636	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2102465	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28770330	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28773028	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28778631	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28825119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28863270	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59912282	0.89[ASN][1000 genomes]
rs60482539	0.85[EUR][1000 genomes]
rs66462353	0.85[EUR][1000 genomes]
rs67505007	0.86[EUR][1000 genomes]
rs7162435	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs7179116	0.83[EUR][1000 genomes]
rs7182397	0.85[EUR][1000 genomes]
rs72734373	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8029247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8032158	0.86[EUR][1000 genomes]
rs8038646	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038884	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920158	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920159	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920184	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904245	chr15:56229760-56324451	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv457159	chr15:56255774-56321854	Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv569543	chr15:56255774-56321854	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12595728	PRTG	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56229600-56282600	Weak transcription	NHLF	lung
2	chr15:56231400-56284200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:56236200-56276000	Weak transcription	HUVEC	blood vessel
4	chr15:56236800-56282800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:56243200-56276200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:56248200-56285200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:56251600-56281600	Weak transcription	Osteobl	bone
8	chr15:56253600-56282400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:56257600-56281600	Weak transcription	Fetal Intestine Large	intestine
10	chr15:56257600-56283600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:56257600-56283800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:56257800-56270200	Weak transcription	Aorta	Aorta
13	chr15:56257800-56273800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:56262600-56269200	Weak transcription	A549	lung
15	chr15:56262800-56274200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:56262800-56276200	Weak transcription	NHEK	skin
17	chr15:56262800-56276400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:56262800-56276600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:56262800-56276600	Weak transcription	HMEC	breast
20	chr15:56263000-56269000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:56263000-56275400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:56263800-56282400	Weak transcription	Fetal Intestine Small	intestine

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