Variant report

Variant	rs28458188
Chromosome Location	chr15:58859890-58859891
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	chr15:58855055..58857360-chr15:58858745..58860281,2	K562	blood:
2	chr15:58858333..58860750-chr15:58870905..58872413,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12908645	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12913969	0.82[EUR][1000 genomes]
rs17301857	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17301864	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242063	0.82[EUR][1000 genomes]
rs2242066	0.82[EUR][1000 genomes]
rs28427123	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28515698	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28524122	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28569241	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28602186	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36017602	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6074	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62005260	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs871804	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv569601	chr15:58800766-58866156	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050231	chr15:58848727-58863526	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1043560	chr15:58851369-58863526	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3312432	chr15:58859060-58860208	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3312433	chr15:58859060-58860208	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58844600-58860400	Weak transcription	Primary T cells from cord blood	blood
2	chr15:58847200-58860400	Weak transcription	Thymus	Thymus
3	chr15:58852400-58860400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:58853200-58865000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:58853600-58860200	Weak transcription	Stomach Mucosa	stomach
6	chr15:58854200-58860400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:58854200-58860400	Weak transcription	Pancreas	Pancrea
8	chr15:58854600-58860400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:58854600-58864200	Weak transcription	HepG2	liver
10	chr15:58854800-58868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:58857800-58860400	Weak transcription	Fetal Thymus	thymus
12	chr15:58857800-58860600	Weak transcription	Fetal Kidney	kidney
13	chr15:58857800-58862800	Weak transcription	Colonic Mucosa	Colon
14	chr15:58858400-58860400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:58858600-58860200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:58858600-58860400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:58859000-58860200	Weak transcription	NHEK	skin
18	chr15:58859000-58865600	Weak transcription	Liver	Liver
19	chr15:58859800-58860000	Enhancers	Adipose Nuclei	Adipose
20	chr15:58859800-58861000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr15:58859800-58861200	Enhancers	K562	blood

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