Variant report

Variant	rs1946733
Chromosome Location	chr4:86966639-86966640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10002407	0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10023731	0.88[ASN][1000 genomes]
rs10027225	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10031752	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10856856	0.83[GIH][hapmap]
rs11929863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12502934	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12512583	0.89[ASN][1000 genomes]
rs13103374	0.96[ASN][1000 genomes]
rs13112959	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13353771	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1469869	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1898248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1898249	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118044	0.92[ASN][1000 genomes]
rs2282596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282597	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282598	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]
rs2589506	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2589515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2589516	0.92[ASN][1000 genomes]
rs28485608	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28516651	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28865277	0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs34998174	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35823399	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3755970	0.86[AFR][1000 genomes]
rs3775167	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775170	0.91[CEU][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775173	0.83[ASW][hapmap]
rs3775182	0.86[CHD][hapmap]
rs3775184	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6822410	0.83[ASN][1000 genomes]
rs6840318	0.92[ASN][1000 genomes]
rs9307015	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9884282	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9884770	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9995879	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[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	nsv998531	chr4:86966103-86980077	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv511259	chr4:86966327-86983232	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1946733	COPS4	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86916800-86985400	Weak transcription	Ovary	ovary
2	chr4:86936000-86975600	Weak transcription	Brain Germinal Matrix	brain
3	chr4:86936400-86990600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:86949200-86988600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:86950600-86967000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:86955000-86985000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:86955200-86971000	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:86955200-87003800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:86956200-86969600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:86958200-86975600	Weak transcription	Fetal Brain Female	brain
11	chr4:86958400-86992600	Weak transcription	Fetal Kidney	kidney
12	chr4:86961200-86979400	Weak transcription	Fetal Stomach	stomach
13	chr4:86961200-86981000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:86963600-86974400	Weak transcription	Fetal Lung	lung
15	chr4:86963600-86988800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:86964600-86966800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:86965200-86968000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:86965200-86968800	Weak transcription	NHDF-Ad	bronchial
19	chr4:86965200-86976200	Weak transcription	Brain Anterior Caudate	brain
20	chr4:86965200-86985800	Weak transcription	Adipose Nuclei	Adipose
21	chr4:86965200-86987000	Weak transcription	Brain Substantia Nigra	brain
22	chr4:86966400-86967200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr4:86966400-86967200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:86966600-86966800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:86966600-86966800	Enhancers	Brain Cingulate Gyrus	brain
26	chr4:86966600-86967000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:86966600-86967000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr4:86966600-86967000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr4:86966600-86967200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:86966600-86967200	Enhancers	HUES48 Cell Line	embryonic stem cell

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