Variant report

Variant	rs28757099
Chromosome Location	chr15:51600117-51600118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51599001..51601083-chr15:51656422..51658497,2	MCF-7	breast:
2	chr15:51599748..51602219-chr15:51603631..51606239,3	MCF-7	breast:
3	chr15:51598697..51600244-chr15:51613341..51616077,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLDN-1	chr15:51600026-51600559	NONHSAT043853

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs28757102	1.00[AFR][1000 genomes]
rs28757114	0.87[AFR][1000 genomes]
rs28757119	0.87[AFR][1000 genomes]
rs28757121	0.81[AFR][1000 genomes]
rs28757124	0.87[AFR][1000 genomes]
rs28757139	0.81[AFR][1000 genomes]
rs35784261	0.87[AFR][1000 genomes]
rs57090104	0.87[AFR][1000 genomes]
rs58724502	0.87[AFR][1000 genomes]
rs9282662	0.87[AFR][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	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51591400-51602800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:51591800-51604600	Weak transcription	Gastric	stomach
3	chr15:51592200-51615000	Weak transcription	Spleen	Spleen
4	chr15:51594600-51602200	Weak transcription	HepG2	liver
5	chr15:51596600-51602000	Weak transcription	Fetal Lung	lung
6	chr15:51599200-51600400	Enhancers	Right Atrium	heart
7	chr15:51599200-51600600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:51599200-51600800	Strong transcription	Placenta	Placenta
9	chr15:51599400-51600400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:51599600-51600200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr15:51599800-51600200	Weak transcription	Adipose Nuclei	Adipose
12	chr15:51599800-51600400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
13	chr15:51599800-51600400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr15:51599800-51600400	Enhancers	Aorta	Aorta
15	chr15:51599800-51600600	Enhancers	HMEC	breast
16	chr15:51599800-51600600	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr15:51600000-51600200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:51600000-51600200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:51600000-51600400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:51600000-51600400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:51600000-51600400	Enhancers	Right Ventricle	heart
22	chr15:51600000-51601200	Enhancers	Left Ventricle	heart
23	chr15:51600000-51602000	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links