Variant report

Variant	rs4285943
Chromosome Location	chr12:45404768-45404769
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10880696	0.80[MEX][hapmap]
rs10880718	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880730	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11182706	0.80[MEX][hapmap]
rs11182801	0.91[JPT][hapmap]
rs11182810	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11182811	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1118481	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1224436	0.94[EUR][1000 genomes]
rs1495033	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1495034	0.94[EUR][1000 genomes]
rs1495035	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495036	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495042	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1506678	0.84[ASW][hapmap];0.85[MKK][hapmap]
rs1857924	0.88[EUR][1000 genomes]
rs1857925	0.88[EUR][1000 genomes]
rs1857926	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2408140	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2544102	0.96[CEU][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs2643140	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs2731040	0.90[EUR][1000 genomes]
rs2731053	0.91[EUR][1000 genomes]
rs2731054	0.91[EUR][1000 genomes]
rs4561266	1.00[CEU][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs7295923	0.86[ASW][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap]
rs7963606	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7964973	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351644	chr12:45345597-45529449	Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1045857	chr12:45351172-45468784	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv541485	chr12:45351172-45468784	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4285943	RP11-478B9.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4285943	CCL1	trans	cerebellum	SCAN
rs4285943	NELL2	cis	Adipose Subcutaneous	GTEx
rs4285943	DBX2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45393000-45412600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:45394600-45406000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:45401600-45405000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:45401800-45404800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:45404400-45404800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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