Variant report

Variant	rs9920827
Chromosome Location	chr15:82476959-82476960
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	chr15:82468744..82470564-chr15:82476578..82478505,2	K562	blood:
2	chr15:82472620..82475056-chr15:82476421..82478115,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1128431	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11852244	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11853682	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11854157	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11855145	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856561	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs16973420	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16973451	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973453	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17354842	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292071	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28529095	0.87[ASN][1000 genomes]
rs28539162	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28578791	0.85[ASN][1000 genomes]
rs28675984	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754625	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28883606	0.82[ASN][1000 genomes]
rs3973890	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4725	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4778983	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55914836	0.90[ASN][1000 genomes]
rs56394250	0.84[ASN][1000 genomes]
rs57014042	0.84[ASN][1000 genomes]
rs60855901	0.90[ASN][1000 genomes]
rs61203524	0.87[ASN][1000 genomes]
rs6495644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66672254	0.88[ASN][1000 genomes]
rs66701409	0.90[ASN][1000 genomes]
rs67988426	0.80[ASN][1000 genomes]
rs71156029	0.88[ASN][1000 genomes]
rs7162177	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73451393	0.86[ASN][1000 genomes]
rs8023960	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs8028284	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs8032033	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8034586	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040160	0.86[ASN][1000 genomes]
rs8042665	0.81[EUR][1000 genomes];0.96[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9920827	RP11-152F13.7	cis	Esophagus Mucosa	GTEx
rs9920827	RP11-152F13.3	cis	Esophagus Mucosa	GTEx
rs9920827	FLJ22795///LOC727751	N/A	lymphoblastoid	RTeQTL
rs9920827	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs9920827	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs9920827	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs9920827	AP3B2	cis	lung	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82432600-82552800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:82444600-82495800	Weak transcription	Fetal Intestine Small	intestine
3	chr15:82456000-82510000	Weak transcription	Thymus	Thymus
4	chr15:82456400-82480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:82456400-82487000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr15:82456400-82502200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr15:82456400-82502400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:82456400-82502600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:82456400-82502800	Weak transcription	Gastric	stomach
10	chr15:82456400-82505400	Weak transcription	Dnd41	blood
11	chr15:82456400-82505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:82456400-82505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:82456600-82478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:82456600-82497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:82456800-82509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:82458200-82504800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:82458600-82479200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:82458800-82502800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:82462000-82505800	Weak transcription	Primary B cells from cord blood	blood
20	chr15:82464000-82494800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:82465000-82510000	Weak transcription	Placenta	Placenta
22	chr15:82471000-82478200	Weak transcription	Esophagus	oesophagus
23	chr15:82471000-82481200	Weak transcription	Aorta	Aorta
24	chr15:82471000-82502200	Weak transcription	NHEK	skin
25	chr15:82471000-82502800	Weak transcription	Fetal Stomach	stomach
26	chr15:82471000-82518600	Weak transcription	Right Ventricle	heart
27	chr15:82471200-82485000	Weak transcription	NHDF-Ad	bronchial
28	chr15:82472200-82480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:82474000-82478600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:82474400-82477000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:82474800-82479000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr15:82474800-82502600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:82474800-82502800	Weak transcription	Fetal Intestine Large	intestine
34	chr15:82475000-82477000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:82475000-82477200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr15:82475000-82477400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr15:82475200-82477000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:82475200-82477000	Strong transcription	Primary T cells from cord blood	blood
39	chr15:82475200-82477000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:82475200-82477000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:82475200-82477000	Enhancers	Liver	Liver
42	chr15:82475200-82477000	Enhancers	HSMMtube	muscle
43	chr15:82475200-82477000	Enhancers	Osteobl	bone
44	chr15:82475200-82477200	Enhancers	Brain Angular Gyrus	brain
45	chr15:82475200-82477200	Enhancers	Brain Substantia Nigra	brain
46	chr15:82475200-82477600	Enhancers	Brain Cingulate Gyrus	brain
47	chr15:82475200-82477600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr15:82475200-82477600	Enhancers	Ovary	ovary
49	chr15:82475200-82477600	Enhancers	Psoas Muscle	Psoas
50	chr15:82475200-82478400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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