Variant report

Variant	rs62012004
Chromosome Location	chr15:82476265-82476266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12902481	1.00[ASN][1000 genomes]
rs17269819	0.88[EUR][1000 genomes]
rs17354185	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17356118	1.00[ASN][1000 genomes]
rs17507216	1.00[ASN][1000 genomes]
rs28470877	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587326	0.82[EUR][1000 genomes]
rs28648832	1.00[ASN][1000 genomes]
rs2867649	0.82[EUR][1000 genomes]
rs28689861	0.82[EUR][1000 genomes]
rs28694364	0.94[EUR][1000 genomes]
rs28697264	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28876157	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34341037	1.00[ASN][1000 genomes]
rs3850610	1.00[ASN][1000 genomes]
rs4778665	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009918	1.00[ASN][1000 genomes]
rs62010071	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012003	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012005	1.00[ASN][1000 genomes]
rs62012010	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012011	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012043	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62012046	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012047	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012049	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012056	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012059	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62013461	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62013464	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67548148	1.00[ASN][1000 genomes]
rs67824562	1.00[ASN][1000 genomes]
rs72751643	1.00[ASN][1000 genomes]
rs7496227	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026737	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034801	0.88[EUR][1000 genomes]
rs9944185	0.87[EUR][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	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv457213	chr15:82456227-82573255	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv570244	chr15:82456227-82573255	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62012004	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs62012004	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs62012004	AP3B2	cis	Artery Tibial	GTEx
rs62012004	AP3B2	cis	Nerve Tibial	GTEx
rs62012004	RP11-152F13.3	cis	lung	GTEx
rs62012004	AP3B2	cis	Whole Blood	GTEx
rs62012004	AP3B2	cis	lung	GTEx
rs62012004	AP3B2	cis	Muscle Skeletal	GTEx
rs62012004	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82432600-82476400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:82432600-82552800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr15:82444600-82495800	Weak transcription	Fetal Intestine Small	intestine
4	chr15:82456000-82510000	Weak transcription	Thymus	Thymus
5	chr15:82456400-82480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:82456400-82487000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr15:82456400-82502200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr15:82456400-82502400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:82456400-82502600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:82456400-82502800	Weak transcription	Gastric	stomach
11	chr15:82456400-82505400	Weak transcription	Dnd41	blood
12	chr15:82456400-82505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:82456400-82505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:82456600-82478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:82456600-82497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:82456800-82509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr15:82458200-82504800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr15:82458600-82479200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr15:82458800-82502800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:82462000-82505800	Weak transcription	Primary B cells from cord blood	blood
21	chr15:82464000-82494800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:82464200-82476600	Weak transcription	Hela-S3	cervix
23	chr15:82465000-82510000	Weak transcription	Placenta	Placenta
24	chr15:82470200-82476600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:82471000-82478200	Weak transcription	Esophagus	oesophagus
26	chr15:82471000-82481200	Weak transcription	Aorta	Aorta
27	chr15:82471000-82502200	Weak transcription	NHEK	skin
28	chr15:82471000-82502800	Weak transcription	Fetal Stomach	stomach
29	chr15:82471000-82518600	Weak transcription	Right Ventricle	heart
30	chr15:82471200-82485000	Weak transcription	NHDF-Ad	bronchial
31	chr15:82472200-82480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:82473000-82476600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:82474000-82478600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:82474400-82477000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:82474800-82479000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr15:82474800-82502600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:82474800-82502800	Weak transcription	Fetal Intestine Large	intestine
38	chr15:82475000-82477000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:82475000-82477200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr15:82475000-82477400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr15:82475200-82476400	Enhancers	Fetal Muscle Leg	muscle
42	chr15:82475200-82476400	Enhancers	Left Ventricle	heart
43	chr15:82475200-82476400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr15:82475200-82476800	Enhancers	Brain Anterior Caudate	brain
45	chr15:82475200-82476800	Enhancers	Fetal Lung	lung
46	chr15:82475200-82476800	Enhancers	Right Atrium	heart
47	chr15:82475200-82476800	Enhancers	NH-A	brain
48	chr15:82475200-82477000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:82475200-82477000	Strong transcription	Primary T cells from cord blood	blood
50	chr15:82475200-82477000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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