Variant report

Variant	rs1877240
Chromosome Location	chr15:83438878-83438879
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83315474..83318164-chr15:83437876..83440206,2	K562	blood:
2	chr15:83438498..83441390-chr15:83475483..83477867,2	K562	blood:
3	chr15:83434319..83435819-chr15:83438378..83440350,2	K562	blood:
4	chr15:83436562..83439014-chr15:83439080..83440888,2	K562	blood:
5	chr15:83315100..83318096-chr15:83438505..83441476,2	K562	blood:
6	chr15:83438774..83441165-chr15:83453782..83456653,2	K562	blood:
7	chr15:83429645..83432307-chr15:83436873..83440129,3	K562	blood:

Variant related genes	Relation type
ENSG00000214575	Chromatin interaction
ENSG00000259462	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12899020	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs12900374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12909628	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12915384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17158396	1.00[CHD][hapmap]
rs36111056	0.92[AFR][1000 genomes]
rs3914699	1.00[CHD][hapmap]
rs4617830	0.89[AFR][1000 genomes]
rs4779033	1.00[CHD][hapmap]
rs7161977	1.00[CHD][hapmap]
rs7163848	1.00[CHD][hapmap];1.00[LWK][hapmap]
rs7165690	1.00[CHD][hapmap]
rs7178859	1.00[CHD][hapmap];0.90[LWK][hapmap]
rs7496832	1.00[CHD][hapmap]
rs8040488	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
6	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
7	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
8	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
9	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
10	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	esv3346074	chr15:83422947-83456222	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1877240	AP3B2	cis	Adipose Subcutaneous	GTEx
rs1877240	AP3B2	cis	Artery Tibial	GTEx
rs1877240	WHAMM	cis	parietal	SCAN
rs1877240	BTBD1	cis	cerebellum	SCAN
rs1877240	AP3B2	cis	Nerve Tibial	GTEx
rs1877240	AP3B2	cis	Thyroid	GTEx
rs1877240	AP3B2	cis	Muscle Skeletal	GTEx
rs1877240	ARNT2	cis	cerebellum	SCAN
rs1877240	DNAJA4	cis	parietal	SCAN
rs1877240	AP3B2	cis	Esophagus Muscularis	GTEx
rs1877240	ACSBG1	cis	cerebellum	SCAN
rs1877240	AP3B2	cis	multi-tissue	Pritchard
rs1877240	AP3B2	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83425000-83447800	Weak transcription	Fetal Brain Male	brain
2	chr15:83427800-83442200	Weak transcription	Brain Substantia Nigra	brain
3	chr15:83428000-83440400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:83428000-83440400	Weak transcription	Esophagus	oesophagus
5	chr15:83428000-83441000	Weak transcription	K562	blood
6	chr15:83428000-83442200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:83428200-83439600	Weak transcription	HMEC	breast
8	chr15:83428200-83440200	Weak transcription	NHEK	skin
9	chr15:83428400-83440200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:83434200-83441200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:83434400-83439000	Weak transcription	Liver	Liver
12	chr15:83434400-83439400	Weak transcription	Gastric	stomach
13	chr15:83434400-83441000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
14	chr15:83434400-83442000	Weak transcription	Pancreas	Pancrea
15	chr15:83434400-83443200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr15:83434600-83439000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
17	chr15:83434600-83442000	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:83434600-83443200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:83434600-83446600	Weak transcription	Fetal Heart	heart
20	chr15:83434800-83443200	Weak transcription	Brain Angular Gyrus	brain
21	chr15:83434800-83443400	Weak transcription	Lung	lung
22	chr15:83434800-83462200	Weak transcription	Ovary	ovary
23	chr15:83435000-83442000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:83435000-83442200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:83435200-83439600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:83435200-83440600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:83435200-83442200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:83435200-83452600	Weak transcription	Fetal Brain Female	brain
29	chr15:83435200-83457000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:83435600-83443400	Strong transcription	Left Ventricle	heart
31	chr15:83436200-83440200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:83436400-83439000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:83436400-83467800	Weak transcription	Psoas Muscle	Psoas
34	chr15:83436600-83445200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:83436800-83439800	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:83436800-83440200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:83436800-83440400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:83436800-83441800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr15:83437000-83448400	Weak transcription	Fetal Stomach	stomach
40	chr15:83437600-83442200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:83437800-83439600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:83437800-83440200	Weak transcription	Right Ventricle	heart
43	chr15:83437800-83453200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr15:83438000-83441400	Weak transcription	HSMM	muscle
45	chr15:83438800-83439000	Active TSS	Spleen	Spleen

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