Variant report

Variant	rs1356421
Chromosome Location	chr12:43143042-43143043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10506219	0.85[EUR][1000 genomes]
rs11181672	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11181673	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11181674	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11181675	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11181676	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11181677	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11181678	0.94[ASW][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11181679	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11181680	0.94[ASW][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11181681	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11181682	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12302566	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12311080	0.85[EUR][1000 genomes]
rs12313884	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12319782	0.86[EUR][1000 genomes]
rs1356422	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1356423	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1914486	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1914487	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1914489	0.90[ASN][1000 genomes]
rs2203734	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2250302	0.94[ASN][1000 genomes]
rs2730983	0.90[ASN][1000 genomes]
rs2897590	0.94[ASW][hapmap];0.91[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57284063	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60367750	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61924560	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61926694	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7137412	0.85[EUR][1000 genomes]
rs7962745	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7963132	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7963276	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs868765	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs870972	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs955918	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832389	chr12:43003361-43173896	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1356421	NELL2	cis	cerebellum	SCAN
rs1356421	IRAK4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43140600-43149600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:43140800-43152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:43142800-43143400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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