Variant report

Variant	rs2469541
Chromosome Location	chr15:76562118-76562119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76561447..76562984-chr15:76571466..76573118,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11072576	0.88[CHB][hapmap]
rs11072579	0.86[CHB][hapmap]
rs11072580	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11072583	0.85[CHB][hapmap]
rs11072585	0.85[CHB][hapmap]
rs11072587	0.86[CHB][hapmap]
rs11634060	0.86[CHB][hapmap]
rs11636851	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12050896	0.85[CHB][hapmap]
rs12438741	0.90[ASN][1000 genomes]
rs12439484	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap]
rs12442266	1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs12592501	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12595211	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12595717	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12595738	0.94[JPT][hapmap]
rs12898415	1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs12901160	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12902506	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12907668	1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs12908334	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12909718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12910640	0.88[JPT][hapmap]
rs12913096	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs12916022	0.91[ASN][1000 genomes]
rs1474117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16968083	0.86[CHB][hapmap]
rs17361504	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1850722	0.86[CHB][hapmap];0.89[MEX][hapmap]
rs1875888	0.84[CHB][hapmap]
rs2139190	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2176623	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs2456045	0.82[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2456046	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs2456050	0.86[CHB][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs2460141	0.82[YRI][hapmap]
rs2460154	0.82[ASW][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2469542	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2469548	0.86[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs2469565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2469566	0.89[ASN][1000 genomes]
rs2959850	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs2959853	0.88[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs34213321	0.91[ASN][1000 genomes]
rs34893715	0.90[ASN][1000 genomes]
rs35707798	0.90[ASN][1000 genomes]
rs35831705	0.81[ASN][1000 genomes]
rs3759853	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3784449	0.86[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs3898352	0.86[CHB][hapmap]
rs4381566	0.80[ASN][1000 genomes]
rs4886484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886485	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4886488	0.89[CHB][hapmap]
rs4886777	0.86[CHB][hapmap];0.90[MEX][hapmap]
rs4886779	0.81[CHB][hapmap];0.90[MEX][hapmap]
rs4886783	0.86[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap]
rs4886787	0.86[CHB][hapmap]
rs4886788	0.86[CHB][hapmap]
rs4886789	0.86[CHB][hapmap];0.90[MEX][hapmap]
rs4886791	0.86[CHB][hapmap];0.90[MEX][hapmap]
rs7163036	0.84[JPT][hapmap]
rs7174889	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7177923	0.86[CHB][hapmap]
rs7180462	0.86[CHB][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap]
rs8028504	0.86[CHB][hapmap];0.84[MEX][hapmap]
rs8029637	0.86[CHB][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap]
rs8030454	0.86[CHB][hapmap]
rs8033494	0.86[CHB][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs869452	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs870295	0.86[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs879625	0.86[CHB][hapmap]
rs883993	0.86[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap]
rs937732	0.90[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap]
rs937733	0.86[CHB][hapmap]
rs959991	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv527608	chr15:76530267-76562738	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2469541	SCAPER	cis	Artery Tibial	GTEx
rs2469541	SCAPER	cis	parietal	SCAN
rs2469541	NRG4	cis	parietal	SCAN
rs2469541	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2469541	SCAPER	cis	cerebellum	SCAN
rs2469541	TBC1D2B	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76550400-76563000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:76550600-76562600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
3	chr15:76550600-76563000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr15:76550600-76563200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:76550600-76563400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:76550600-76563400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:76550600-76563600	ZNF genes & repeats	Fetal Intestine Small	intestine
8	chr15:76550600-76564000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr15:76550600-76578400	Strong transcription	Liver	Liver
10	chr15:76553400-76562800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:76553400-76563200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
12	chr15:76553600-76563200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:76553800-76562600	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr15:76553800-76564200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:76554000-76563800	ZNF genes & repeats	Dnd41	blood
16	chr15:76554200-76562600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr15:76554200-76562600	ZNF genes & repeats	Fetal Lung	lung
18	chr15:76554600-76563000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr15:76555000-76562600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:76555000-76563200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:76555200-76562800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:76555800-76563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:76555800-76564200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:76555800-76564400	Weak transcription	Right Ventricle	heart
25	chr15:76555800-76567200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:76555800-76574200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr15:76555800-76578800	Weak transcription	Psoas Muscle	Psoas
28	chr15:76555800-76579000	Weak transcription	NHLF	lung
29	chr15:76555800-76586000	Weak transcription	Stomach Mucosa	stomach
30	chr15:76556000-76563600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:76556000-76564000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:76556200-76563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:76556200-76565200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:76556200-76569800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:76556400-76581400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:76556800-76594600	Weak transcription	Esophagus	oesophagus
37	chr15:76557000-76567200	Strong transcription	Hela-S3	cervix
38	chr15:76557000-76582800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr15:76557200-76563200	ZNF genes & repeats	GM12878-XiMat	blood
40	chr15:76557600-76562200	Weak transcription	NH-A	brain
41	chr15:76557600-76573400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:76558000-76564400	Weak transcription	NHDF-Ad	bronchial
43	chr15:76558000-76603000	Weak transcription	Aorta	Aorta
44	chr15:76558200-76565000	Strong transcription	Primary T cells from cord blood	blood
45	chr15:76558400-76568200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:76558600-76562200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
47	chr15:76558800-76562600	Weak transcription	HMEC	breast
48	chr15:76558800-76563000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
49	chr15:76559000-76562400	Weak transcription	NHEK	skin
50	chr15:76559200-76562800	Strong transcription	Placenta	Placenta

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