Variant report

Variant	rs28728383
Chromosome Location	chr15:58939451-58939452
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	chr15:58939363..58941206-chr15:59062666..59064194,2	MCF-7	breast:
2	chr15:58938038..58940430-chr15:58949050..58951838,2	K562	blood:

Variant related genes	Relation type
ENSG00000128923	Chromatin interaction
ENSG00000245975	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12438810	0.81[EUR][1000 genomes]
rs12442451	0.83[EUR][1000 genomes]
rs12591543	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12592332	0.86[EUR][1000 genomes]
rs12708455	0.82[EUR][1000 genomes]
rs12906705	0.86[EUR][1000 genomes]
rs12912286	0.88[EUR][1000 genomes]
rs12915950	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12916010	0.80[AMR][1000 genomes]
rs16940589	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16940647	0.82[EUR][1000 genomes]
rs16940651	0.83[EUR][1000 genomes]
rs17301905	0.83[EUR][1000 genomes]
rs1820548	0.80[AMR][1000 genomes]
rs2303532	0.85[EUR][1000 genomes]
rs28455654	0.83[EUR][1000 genomes]
rs28457680	0.80[AMR][1000 genomes]
rs28542491	0.83[EUR][1000 genomes]
rs28600144	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28609304	0.83[EUR][1000 genomes]
rs28637832	0.83[EUR][1000 genomes]
rs28639679	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28724298	0.86[EUR][1000 genomes]
rs35499736	0.81[EUR][1000 genomes]
rs6494030	0.85[EUR][1000 genomes]
rs6494031	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6494032	0.86[EUR][1000 genomes]
rs7163733	0.82[EUR][1000 genomes]
rs7164620	0.80[AMR][1000 genomes]
rs7165035	0.80[AMR][1000 genomes]
rs7165402	0.81[EUR][1000 genomes]
rs7167528	0.83[EUR][1000 genomes]
rs7180550	0.81[EUR][1000 genomes]
rs8026668	0.83[EUR][1000 genomes]
rs8035960	0.86[EUR][1000 genomes]
rs8036005	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8039791	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8040358	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9302203	0.83[EUR][1000 genomes]
rs9744518	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9920042	0.80[AMR][1000 genomes]
rs9920310	0.88[EUR][1000 genomes]
rs9920720	0.83[EUR][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	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	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv569602	chr15:58914326-58964437	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
3	chr15:58905400-58971800	Weak transcription	Spleen	Spleen
4	chr15:58905600-58976400	Weak transcription	Gastric	stomach
5	chr15:58906400-58976400	Weak transcription	Small Intestine	intestine
6	chr15:58907800-58952000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:58911600-58951200	Weak transcription	Fetal Brain Male	brain
8	chr15:58911600-58958000	Weak transcription	Fetal Brain Female	brain
9	chr15:58914200-58957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:58914600-58957000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:58917000-58959600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:58919800-58959200	Weak transcription	Brain Germinal Matrix	brain
13	chr15:58920200-58946600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:58920200-58957200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:58921000-58957600	Weak transcription	Colonic Mucosa	Colon
16	chr15:58921200-58946400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:58921200-58946600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:58921200-58946800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:58921200-58949400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:58921200-58959600	Weak transcription	Aorta	Aorta
21	chr15:58921200-58968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:58921600-58942400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:58921600-58946600	Weak transcription	Fetal Intestine Small	intestine
24	chr15:58921600-58959200	Weak transcription	NHLF	lung
25	chr15:58921600-58976600	Weak transcription	Right Ventricle	heart
26	chr15:58921800-58946400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:58921800-58947200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:58921800-58970400	Weak transcription	Stomach Mucosa	stomach
29	chr15:58922200-58959000	Weak transcription	HUVEC	blood vessel
30	chr15:58922400-58942600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:58923400-58942400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:58923400-58971800	Weak transcription	Pancreas	Pancrea
33	chr15:58923400-58982800	Weak transcription	Lung	lung
34	chr15:58923800-58947400	Weak transcription	Fetal Stomach	stomach
35	chr15:58924000-58960000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:58926400-58957600	Weak transcription	Brain Substantia Nigra	brain
37	chr15:58927000-58956600	Weak transcription	Ovary	ovary
38	chr15:58927200-58940600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:58928200-58941200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr15:58928800-58939600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:58930000-58946600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:58931600-58946600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:58931800-58942400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:58932000-58940200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:58933000-58949600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:58933200-58946600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:58933200-58947000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:58933200-58952400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:58933400-58946600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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