Variant report

Variant	rs28757090
Chromosome Location	chr15:51606592-51606593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:51606027-51608312	HepG2	liver:	n/a	n/a
2	CEBPB	chr15:51605860-51606878	HepG2	liver:	n/a	chr15:51606032-51606045

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51606490..51608990-chr15:51658580..51661011,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259306	TF binding region
ENSG00000259194	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs28757075	1.00[ASW][hapmap]
rs28757102	1.00[ASW][hapmap]
rs28757114	1.00[ASW][hapmap]
rs28757119	1.00[ASW][hapmap]
rs28757121	1.00[ASW][hapmap]
rs28757124	1.00[ASW][hapmap]
rs28757139	1.00[ASW][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28757090	PTPN20B	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51592200-51615000	Weak transcription	Spleen	Spleen
2	chr15:51600400-51614200	Weak transcription	Right Atrium	heart
3	chr15:51601800-51607600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:51602000-51607200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:51602400-51606800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:51603000-51610400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:51603600-51612600	Enhancers	Fetal Intestine Small	intestine
8	chr15:51604000-51612200	Enhancers	Fetal Intestine Large	intestine
9	chr15:51604200-51607600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr15:51604200-51609000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:51605000-51615200	Weak transcription	Left Ventricle	heart
12	chr15:51605200-51610600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:51605200-51610600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:51605400-51607000	Strong transcription	Placenta	Placenta
15	chr15:51605600-51607200	Weak transcription	Fetal Lung	lung
16	chr15:51605600-51608800	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:51605600-51610600	Weak transcription	Osteobl	bone
18	chr15:51606200-51606600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:51606200-51607000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:51606200-51608200	Flanking Active TSS	HepG2	liver
21	chr15:51606400-51606800	Weak transcription	Right Ventricle	heart
22	chr15:51606400-51608000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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