Variant report

Variant	rs28697264
Chromosome Location	chr15:82557900-82557901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:82557073..82558574-chr15:82565794..82567576,2	K562	blood:
2	chr15:82557636..82558140-chr15:84740091..84741075,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs17354185	1.00[ASN][1000 genomes]
rs17356118	1.00[ASN][1000 genomes]
rs17507216	1.00[ASN][1000 genomes]
rs28470877	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542747	0.87[EUR][1000 genomes]
rs28648832	1.00[ASN][1000 genomes]
rs2867649	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28694364	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28876157	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850610	1.00[ASN][1000 genomes]
rs4778665	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778672	0.84[EUR][1000 genomes]
rs4778989	0.89[EUR][1000 genomes]
rs56042848	0.80[EUR][1000 genomes]
rs62009918	1.00[ASN][1000 genomes]
rs62010071	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011975	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012003	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012004	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012005	1.00[ASN][1000 genomes]
rs62012010	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012011	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012043	1.00[ASN][1000 genomes]
rs62012044	0.80[EUR][1000 genomes]
rs62012046	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012047	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012049	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012056	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012059	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62013461	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62013464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165536	0.89[EUR][1000 genomes]
rs72751643	1.00[ASN][1000 genomes]
rs7496227	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
8	nsv570246	chr15:82485707-82581264	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1041506	chr15:82496164-82581427	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv1798145	chr15:82506790-82581264	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv904440	chr15:82524544-82591082	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv904441	chr15:82532963-82580736	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv904442	chr15:82540174-82571046	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1054025	chr15:82540486-83058214	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv904443	chr15:82553472-82571780	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs28697264	AP3B2	cis	lung	GTEx
rs28697264	RP11-152F13.3	cis	lung	GTEx
rs28697264	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs28697264	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs28697264	AP3B2	cis	Artery Tibial	GTEx
rs28697264	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs28697264	AP3B2	cis	Nerve Tibial	GTEx
rs28697264	AP3B2	cis	Muscle Skeletal	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82555400-82565400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:82555800-82558800	Weak transcription	Primary T cells from cord blood	blood
3	chr15:82555800-82558800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:82555800-82559400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:82555800-82560200	Weak transcription	Thymus	Thymus
6	chr15:82555800-82561200	Weak transcription	Fetal Thymus	thymus
7	chr15:82555800-82566400	Weak transcription	Ovary	ovary
8	chr15:82556000-82558200	Weak transcription	Fetal Stomach	stomach
9	chr15:82556000-82558400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:82556000-82558400	Weak transcription	Primary B cells from cord blood	blood
11	chr15:82556000-82558400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr15:82556000-82558600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:82556000-82558600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:82556000-82558600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:82556000-82558600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:82556000-82558600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:82556000-82558600	Weak transcription	Fetal Heart	heart
18	chr15:82556000-82558600	Weak transcription	GM12878-XiMat	blood
19	chr15:82556000-82558600	Weak transcription	HUVEC	blood vessel
20	chr15:82556000-82558800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:82556000-82558800	Weak transcription	Stomach Mucosa	stomach
22	chr15:82556000-82558800	Weak transcription	NHEK	skin
23	chr15:82556000-82559400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr15:82556000-82559400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:82556000-82559600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:82556000-82559600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:82556000-82559600	Weak transcription	HMEC	breast
28	chr15:82556000-82560800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:82556000-82561000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:82556000-82561200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:82556000-82561400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:82556000-82561600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:82556000-82563200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:82556000-82566400	Weak transcription	Fetal Lung	lung
35	chr15:82556200-82558600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:82556200-82558600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr15:82556200-82558600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:82556200-82560000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:82556200-82560600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:82556200-82567400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:82556400-82558600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:82556800-82558600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:82556800-82560600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:82557200-82558600	Weak transcription	K562	blood

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