Variant report

Variant	rs2274892
Chromosome Location	chr17:16852027-16852028
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11651242	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11656532	0.81[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12603708	0.86[CHB][hapmap];0.94[CHD][hapmap]
rs12938061	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs12938073	0.95[CEU][hapmap]
rs34806035	0.96[ASN][1000 genomes]
rs3818716	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383187	0.92[CHD][hapmap]
rs4404112	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs4792801	0.83[CEU][hapmap]
rs8078529	0.84[EUR][1000 genomes]
rs9797203	0.96[ASN][1000 genomes]
rs9893403	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv833379	chr17:16683585-16859539	Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1055688	chr17:16800788-16868860	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv907726	chr17:16821204-16875636	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2274892	COPS3	cis	parietal	SCAN
rs2274892	LOC96597	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16851400-16853000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
2	chr17:16851600-16852400	ZNF genes & repeats	Spleen	Spleen
3	chr17:16851800-16852400	ZNF genes & repeats	Brain Anterior Caudate	brain
4	chr17:16851800-16853000	ZNF genes & repeats	Primary B cells from cord blood	blood
5	chr17:16852000-16852200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:16852000-16852400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:16852000-16852400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
8	chr17:16852000-16852400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:16852000-16852400	ZNF genes & repeats	Brain Substantia Nigra	brain
10	chr17:16852000-16852800	ZNF genes & repeats	Brain Hippocampus Middle	brain
11	chr17:16852000-16853000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
12	chr17:16852000-16857000	ZNF genes & repeats	GM12878-XiMat	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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