Variant report

Variant	rs2867579
Chromosome Location	chr15:82475384-82475385
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1045508	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11073035	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1174543	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1174546	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855089	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11855144	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11857208	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12443224	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12905578	0.88[ASN][1000 genomes]
rs13380317	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13380319	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1392976	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1501371	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1501372	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1846911	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2047678	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2088858	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2455717	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28540744	0.91[ASN][1000 genomes]
rs2867577	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3858954	0.89[ASN][1000 genomes]
rs4270132	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4344697	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4778982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495642	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6495643	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495647	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7164362	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166570	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7169961	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173852	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7176075	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180584	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7181655	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8025353	0.87[ASN][1000 genomes]
rs8033050	0.91[ASN][1000 genomes]
rs8033831	0.82[EUR][1000 genomes]
rs8037224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8041868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041924	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8043108	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs867370	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs867371	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs881308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944197	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2867579	GOLGA6L10	cis	Esophagus Mucosa	GTEx
rs2867579	RP13-608F4.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:86 , 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	chr15:82456000-82475800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:82456000-82475800	Weak transcription	Lung	lung
6	chr15:82456000-82510000	Weak transcription	Thymus	Thymus
7	chr15:82456200-82475600	Weak transcription	Fetal Brain Female	brain
8	chr15:82456400-82475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:82456400-82475800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr15:82456400-82480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:82456400-82487000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr15:82456400-82502200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr15:82456400-82502400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:82456400-82502600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:82456400-82502800	Weak transcription	Gastric	stomach
16	chr15:82456400-82505400	Weak transcription	Dnd41	blood
17	chr15:82456400-82505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:82456400-82505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:82456600-82478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:82456600-82497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:82456800-82509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:82458200-82504800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr15:82458600-82475600	Weak transcription	GM12878-XiMat	blood
24	chr15:82458600-82479200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:82458800-82502800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:82462000-82475800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:82462000-82505800	Weak transcription	Primary B cells from cord blood	blood
28	chr15:82464000-82475400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:82464000-82494800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:82464200-82476600	Weak transcription	Hela-S3	cervix
31	chr15:82465000-82510000	Weak transcription	Placenta	Placenta
32	chr15:82470200-82476600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:82471000-82475400	Weak transcription	Fetal Heart	heart
34	chr15:82471000-82475600	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:82471000-82478200	Weak transcription	Esophagus	oesophagus
36	chr15:82471000-82481200	Weak transcription	Aorta	Aorta
37	chr15:82471000-82502200	Weak transcription	NHEK	skin
38	chr15:82471000-82502800	Weak transcription	Fetal Stomach	stomach
39	chr15:82471000-82518600	Weak transcription	Right Ventricle	heart
40	chr15:82471200-82475400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:82471200-82475800	Weak transcription	NHLF	lung
42	chr15:82471200-82476200	Weak transcription	HMEC	breast
43	chr15:82471200-82485000	Weak transcription	NHDF-Ad	bronchial
44	chr15:82472200-82480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:82473000-82476600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:82474000-82478600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:82474200-82475400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:82474200-82475400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:82474200-82475800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:82474400-82477000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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