Variant report

Variant	rs8040488
Chromosome Location	chr15:83367833-83367834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83366323..83369466-chr15:83375659..83378922,4	K562	blood:
2	chr15:83366884..83369469-chr15:83380434..83383177,2	MCF-7	breast:
3	chr15:83241058..83243039-chr15:83367492..83370195,2	K562	blood:
4	chr15:83348154..83351401-chr15:83364138..83368453,6	MCF-7	breast:
5	chr15:83366312..83369718-chr15:83416708..83419690,4	MCF-7	breast:
6	chr15:83348031..83349686-chr15:83366769..83368430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228141	Chromatin interaction
ENSG00000214575	Chromatin interaction
ENSG00000250988	Chromatin interaction
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12900374	1.00[CHD][hapmap]
rs12915384	1.00[CHD][hapmap]
rs1431716	0.85[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17158396	1.00[CHD][hapmap]
rs17507216	0.82[GIH][hapmap];0.82[MEX][hapmap]
rs1877240	1.00[CHD][hapmap]
rs28371837	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28607761	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28737193	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28833239	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28864981	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28877110	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28888975	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35728728	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3850610	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs3914699	1.00[CHD][hapmap]
rs4513065	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4627310	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4779033	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs4779034	0.85[CEU][hapmap]
rs4779035	0.92[YRI][hapmap]
rs7161977	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7163848	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs7165690	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7178859	1.00[CHD][hapmap]
rs72751675	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7496832	1.00[CHD][hapmap]
rs8028130	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs8032321	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs8040488	AP3B2	cis	Thyroid	GTEx
rs8040488	AP3B2	cis	lung	GTEx
rs8040488	ACSBG1	cis	cerebellum	SCAN
rs8040488	AP3B2	cis	Muscle Skeletal	GTEx
rs8040488	AP3B2	cis	Esophagus Mucosa	GTEx
rs8040488	AP3B2	cis	Esophagus Muscularis	GTEx
rs8040488	FAM154B	cis	parietal	SCAN
rs8040488	AP3B2	cis	Artery Tibial	GTEx
rs8040488	AP3B2	cis	Adipose Subcutaneous	GTEx
rs8040488	AP3B2	cis	cerebellum	SCAN
rs8040488	AP3B2	cis	Skin Sun Exposed Lower leg	GTEx
rs8040488	CPEB1	cis	lymphoblastoid	seeQTL
rs8040488	AP3B2	cis	Nerve Tibial	GTEx
rs8040488	RP11-152F13.3	cis	lung	GTEx
rs8040488	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs8040488	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs8040488	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83349800-83377200	Weak transcription	Brain Anterior Caudate	brain
2	chr15:83350400-83368000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:83350400-83369800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:83350400-83372800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:83350600-83368400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:83350600-83369000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:83351600-83377200	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:83351800-83377200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:83351800-83377400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:83355600-83368600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:83357600-83368200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:83357800-83368800	Weak transcription	Brain Angular Gyrus	brain
13	chr15:83358200-83377200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:83363000-83370400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:83364200-83369000	Strong transcription	Fetal Brain Female	brain
16	chr15:83365200-83371000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:83365400-83376600	Weak transcription	Fetal Brain Male	brain
18	chr15:83366400-83369000	Strong transcription	Brain Germinal Matrix	brain
19	chr15:83367400-83368800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:83367600-83368400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:83367600-83368400	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr15:83367600-83369200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr15:83367600-83370000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:83367600-83370200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:83367800-83368000	Enhancers	K562	blood
26	chr15:83367800-83368600	Strong transcription	Brain Cingulate Gyrus	brain

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