Variant report

Variant	rs12141269
Chromosome Location	chr1:46705106-46705107
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	chr1:46704725..46706632-chr1:46709197..46711937,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10489770	1.00[ASW][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs10789488	0.92[JPT][hapmap];1.00[MEX][hapmap]
rs10890384	0.89[CHB][hapmap]
rs10890386	0.92[JPT][hapmap];1.00[MEX][hapmap]
rs10890388	1.00[MEX][hapmap]
rs12028248	0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs12125573	1.00[MEX][hapmap]
rs12126187	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12141928	0.89[CHB][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes]
rs12406217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1547180	1.00[MEX][hapmap]
rs17102087	0.89[CHB][hapmap]
rs4612574	0.84[AMR][1000 genomes]
rs4660918	1.00[MEX][hapmap]
rs4660919	1.00[MEX][hapmap]
rs4660921	1.00[MEX][hapmap]
rs6429594	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6689182	0.88[MEX][hapmap]
rs6692775	0.89[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs6696085	0.89[CHB][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs7552312	0.89[CHB][hapmap]
rs953070	0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12141269	NSUN4	cis	parietal	SCAN
rs12141269	MMACHC	cis	cerebellum	SCAN
rs12141269	CYP4Z1	cis	parietal	SCAN
rs12141269	SNORD55	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46673000-46712200	Weak transcription	Right Atrium	heart
2	chr1:46704200-46705200	Enhancers	NHDF-Ad	bronchial
3	chr1:46704200-46705400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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