Variant report

Variant	rs28371837
Chromosome Location	chr15:83383187-83383188
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000228141	TF binding region
AP3B2	TF binding region
ENSG00000259707	Chromatin interaction
ENSG00000103723	Chromatin interaction
ENSG00000250988	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1431716	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28607761	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28737193	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28833239	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28864981	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28877110	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28888975	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35728728	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4513065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7161977	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7163848	0.81[EUR][1000 genomes]
rs7165690	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72751675	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8028130	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8032321	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8040488	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv904450	chr15:83347193-83395340	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs28371837	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs28371837	AP3B2	cis	Esophagus Muscularis	GTEx
rs28371837	AP3B2	cis	Thyroid	GTEx
rs28371837	AP3B2	cis	Artery Tibial	GTEx
rs28371837	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs28371837	AP3B2	cis	Whole Blood	GTEx
rs28371837	AP3B2	cis	Adipose Subcutaneous	GTEx
rs28371837	AP3B2	cis	Skin Sun Exposed Lower leg	GTEx
rs28371837	AP3B2	cis	lung	GTEx
rs28371837	AP3B2	cis	Nerve Tibial	GTEx
rs28371837	AP3B2	cis	Muscle Skeletal	GTEx
rs28371837	AP3B2	cis	Esophagus Mucosa	GTEx
rs28371837	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83382400-83383600	Enhancers	GM12878-XiMat	blood
2	chr15:83382600-83383200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:83382600-83384200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:83382600-83384400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr15:83382800-83384000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:83383000-83383800	Enhancers	Primary hematopoietic stem cells	blood

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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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