Variant report

Variant	rs56273246
Chromosome Location	chr15:45740911-45740912
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	MAZ	chr15:45740256-45741095	Hela-S3	cervix:	n/a	chr15:45740646-45740656
2	MAZ	chr15:45740084-45741150	IMR90	lung:	n/a	chr15:45740646-45740656
3	MAX	chr15:45740256-45741043	Hela-S3	cervix:	n/a	chr15:45740646-45740656
4	SMARCC1	chr15:45740184-45741352	Hela-S3	cervix:	n/a	chr15:45740463-45740472
5	ZKSCAN1	chr15:45740580-45740920	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:45740768-45741089	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45736069..45742318-chr15:45926037..45929619,6	MCF-7	breast:
2	chr15:45740795..45743926-chr15:45878461..45880935,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf48-1	chr15:45740625-45740999	ENSG00000259354.1

Variant related genes	Relation type
ENSG00000259354	TF binding region
RNU7-5P	TF binding region
ENSG00000104164	Chromatin interaction
ENSG00000137767	Chromatin interaction
ENSG00000260170	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10152337	0.96[ASN][1000 genomes]
rs10152697	0.96[ASN][1000 genomes]
rs10851425	0.99[EUR][1000 genomes]
rs12324848	0.96[ASN][1000 genomes]
rs1288852	0.94[EUR][1000 genomes]
rs1288861	0.98[ASN][1000 genomes]
rs1288863	0.99[EUR][1000 genomes]
rs1288865	0.98[EUR][1000 genomes]
rs16942066	0.87[ASN][1000 genomes]
rs1706799	0.85[ASN][1000 genomes]
rs17533716	0.85[ASN][1000 genomes]
rs17535381	0.96[ASN][1000 genomes]
rs17537244	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17618294	0.96[ASN][1000 genomes]
rs2433602	0.98[ASN][1000 genomes]
rs2453518	0.94[EUR][1000 genomes]
rs2453546	0.98[ASN][1000 genomes]
rs2461706	0.98[ASN][1000 genomes]
rs2486287	0.98[ASN][1000 genomes]
rs2668746	0.83[ASN][1000 genomes]
rs55721266	0.96[ASN][1000 genomes]
rs55904415	0.96[ASN][1000 genomes]
rs56267974	0.98[ASN][1000 genomes]
rs56306977	0.98[ASN][1000 genomes]
rs56327050	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56937414	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56967490	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57369693	0.96[ASN][1000 genomes]
rs57419781	0.96[ASN][1000 genomes]
rs61301536	0.98[ASN][1000 genomes]
rs72709081	0.87[ASN][1000 genomes]
rs72709084	0.87[ASN][1000 genomes]
rs72709088	0.96[ASN][1000 genomes]
rs72711253	0.98[ASN][1000 genomes]
rs72711255	0.98[ASN][1000 genomes]
rs72711259	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972405	0.96[ASN][1000 genomes]
rs9972498	0.96[ASN][1000 genomes]
rs9972528	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer 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	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv442701	chr15:45737096-45748752	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45738200-45746600	Weak transcription	Osteobl	bone
2	chr15:45738400-45742000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:45738400-45742000	Enhancers	Stomach Mucosa	stomach
4	chr15:45739000-45741400	Weak transcription	Liver	Liver
5	chr15:45739200-45742000	Weak transcription	Pancreas	Pancrea
6	chr15:45740000-45741600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr15:45740200-45741000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:45740200-45741000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:45740200-45741000	Enhancers	Esophagus	oesophagus
10	chr15:45740200-45741000	Enhancers	Lung	lung
11	chr15:45740200-45741000	Enhancers	Small Intestine	intestine
12	chr15:45740200-45741000	Enhancers	HSMMtube	muscle
13	chr15:45740200-45741000	Enhancers	NHDF-Ad	bronchial
14	chr15:45740200-45741200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:45740200-45741200	Enhancers	NH-A	brain
16	chr15:45740200-45741400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:45740200-45741400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:45740200-45741400	Enhancers	Placenta	Placenta
19	chr15:45740200-45741400	Enhancers	Gastric	stomach
20	chr15:45740200-45741600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:45740200-45742000	Enhancers	Duodenum Mucosa	Duodenum
22	chr15:45740400-45741000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:45740400-45741000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:45740400-45741000	Enhancers	Spleen	Spleen
25	chr15:45740400-45741200	Enhancers	HSMM	muscle
26	chr15:45740400-45741400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr15:45740400-45741400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr15:45740400-45741400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:45740400-45741400	Flanking Active TSS	Hela-S3	cervix
30	chr15:45740400-45742000	Enhancers	Fetal Intestine Large	intestine
31	chr15:45740400-45742000	Enhancers	Fetal Intestine Small	intestine
32	chr15:45740400-45743000	Enhancers	Placenta Amnion	Placenta Amnion
33	chr15:45740600-45741000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr15:45740600-45741000	Flanking Active TSS	A549	lung
35	chr15:45740600-45741200	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr15:45740600-45741600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr15:45740600-45742000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:45740600-45742200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr15:45740600-45743200	Bivalent Enhancer	HepG2	liver
40	chr15:45740800-45741000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr15:45740800-45741200	Enhancers	Colonic Mucosa	Colon
42	chr15:45740800-45741400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr15:45740800-45741400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
44	chr15:45740800-45742200	Weak transcription	HMEC	breast
45	chr15:45740800-45742400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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