Variant report

Variant	rs12644947
Chromosome Location	chr4:87021938-87021939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10001162	0.97[ASN][1000 genomes]
rs10009993	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10028075	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1010778	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs10856856	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11097091	0.97[ASN][1000 genomes]
rs11097092	0.97[ASN][1000 genomes]
rs11934691	0.90[ASN][1000 genomes]
rs12502902	0.98[ASN][1000 genomes]
rs12502934	0.95[GIH][hapmap]
rs12644938	0.88[ASN][1000 genomes]
rs13112959	0.90[GIH][hapmap]
rs1436521	0.97[ASN][1000 genomes]
rs1436527	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1469869	0.90[GIH][hapmap]
rs2589514	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3775181	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3775183	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3775187	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4133139	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4364253	0.97[ASN][1000 genomes]
rs4482754	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4487330	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4501213	0.98[ASN][1000 genomes]
rs6531896	0.88[ASN][1000 genomes]
rs6810413	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7692676	0.88[ASN][1000 genomes]
rs9884770	0.95[GIH][hapmap]
rs9995879	0.93[GIH][hapmap]
rs9996208	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2754254	chr4:86979147-87108510	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv879521	chr4:86979927-87165758	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12644947	COPS4	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87004000-87028400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:87005000-87050400	Weak transcription	Brain Angular Gyrus	brain
3	chr4:87005400-87028200	Weak transcription	Ovary	ovary
4	chr4:87005400-87028400	Weak transcription	Fetal Stomach	stomach
5	chr4:87005600-87023000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:87005600-87026200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:87005600-87031200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:87005600-87035200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:87009200-87027400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:87010800-87035800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:87011400-87035600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:87011600-87023000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:87011800-87028400	Weak transcription	Fetal Lung	lung
14	chr4:87015600-87024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:87015800-87024400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:87016600-87028200	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:87020800-87022200	Weak transcription	Fetal Brain Male	brain
18	chr4:87021400-87023400	Enhancers	Pancreatic Islets	Pancreatic Islet

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