Variant report

Variant	rs2282598
Chromosome Location	chr4:86952923-86952924
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	chr4:86951249..86952929-chr4:86954553..86956104,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10002407	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10023731	0.84[ASN][1000 genomes]
rs10027225	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10031752	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11929863	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12502934	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12512583	0.85[ASN][1000 genomes]
rs13103374	0.92[ASN][1000 genomes]
rs13112959	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13353771	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1469869	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1898248	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1898249	0.92[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1946733	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2118044	0.88[ASN][1000 genomes]
rs2282596	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2282597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2575675	0.87[CHD][hapmap]
rs2589506	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2589515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2589516	0.96[ASN][1000 genomes]
rs28485608	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28516651	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28865277	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34998174	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35823399	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755970	0.87[AFR][1000 genomes]
rs3775167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775170	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775173	0.83[ASW][hapmap]
rs3775184	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811151	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6840318	0.88[ASN][1000 genomes]
rs7699978	0.87[CHD][hapmap]
rs9307015	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9884282	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9884770	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9995879	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2282598	COQ2	cis	cerebellum	SCAN
rs2282598	COPS4	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86916800-86985400	Weak transcription	Ovary	ovary
2	chr4:86917000-86954000	Weak transcription	Pancreas	Pancrea
3	chr4:86928600-86953400	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:86932800-86953800	Weak transcription	Fetal Lung	lung
5	chr4:86934200-86953400	Weak transcription	Aorta	Aorta
6	chr4:86936000-86975600	Weak transcription	Brain Germinal Matrix	brain
7	chr4:86936400-86954600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:86936400-86990600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:86936800-86953600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:86938200-86954200	Weak transcription	Fetal Kidney	kidney
11	chr4:86938400-86953400	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:86938600-86953400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:86938600-86953600	Weak transcription	Brain Angular Gyrus	brain
14	chr4:86938600-86954000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:86938600-86957800	Weak transcription	Fetal Brain Female	brain
16	chr4:86939200-86953800	Weak transcription	Fetal Stomach	stomach
17	chr4:86944600-86954200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:86944600-86963000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:86945400-86963200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:86946400-86954000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:86946600-86953200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:86948200-86953800	Weak transcription	Lung	lung
23	chr4:86948200-86966600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:86948600-86953400	Weak transcription	Left Ventricle	heart
25	chr4:86949200-86988600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:86949400-86953600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:86950600-86959200	Weak transcription	Fetal Brain Male	brain
28	chr4:86950600-86967000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:86952200-86956000	Weak transcription	Spleen	Spleen
30	chr4:86952400-86953000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:86952600-86953600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:86952600-86953600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:86952600-86956400	Enhancers	Fetal Heart	heart
34	chr4:86952800-86953400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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