Variant report

Variant	rs2440315
Chromosome Location	chr15:53084353-53084354
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ONECUT1	TF binding region
ENSG00000170919	Chromatin interaction
ENSG00000273149	Chromatin interaction
ENSG00000169856	Chromatin interaction
ENSG00000133112	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1899752	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs2120442	0.81[TSI][hapmap]
rs2165991	0.81[CEU][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs2244272	0.84[TSI][hapmap]
rs2440316	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440374	0.90[EUR][1000 genomes]
rs2456506	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2456523	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2456525	0.95[ASN][1000 genomes]
rs2456531	0.95[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2460	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28687152	0.94[EUR][1000 genomes]
rs60065065	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7180600	0.92[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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv457142	chr15:53041887-53091896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	nsv569427	chr15:53041887-53091896	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
5	nsv1046970	chr15:53065114-53142386	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	nsv569428	chr15:53069874-53140045	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53083600-53088400	Weak transcription	Pancreas	Pancrea
2	chr15:53083600-53088600	Weak transcription	Liver	Liver
3	chr15:53084000-53084400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:53084000-53084400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:53084000-53086800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr15:53084000-53086800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr15:53084000-53086800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
8	chr15:53084200-53084400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr15:53084200-53084400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
10	chr15:53084200-53084600	Bivalent Enhancer	Stomach Mucosa	stomach
11	chr15:53084200-53086200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
12	chr15:53084200-53086600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr15:53084200-53086800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
14	chr15:53084200-53086800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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