Variant report

Variant	rs1539052
Chromosome Location	chr1:58044501-58044502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11585229	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12564935	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12733015	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357785	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1357787	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1404390	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1608691	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs17116025	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691439	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2691461	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793627	1.00[JPT][hapmap]
rs2793632	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2793633	1.00[JPT][hapmap]
rs2805847	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2805848	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2805852	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35023196	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527457	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530027	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540619	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541243	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv523574	chr1:58018103-58087789	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv871684	chr1:58021206-58096379	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58039200-58046800	Enhancers	Stomach Mucosa	stomach
2	chr1:58042000-58044800	Enhancers	Duodenum Mucosa	Duodenum
3	chr1:58042800-58051600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:58043800-58044800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:58044200-58045000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:58044400-58044800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr1:58044400-58045200	Enhancers	HUES48 Cell Line	embryonic stem cell

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