Variant report

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10784882	0.83[ASN][1000 genomes]
rs10784901	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10879259	0.81[ASN][1000 genomes]
rs10879294	0.80[EUR][1000 genomes]
rs11178530	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11178540	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11178848	0.80[EUR][1000 genomes]
rs1584096	0.89[ASN][1000 genomes]
rs1584097	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1822598	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1854481	0.97[ASN][1000 genomes]
rs1854482	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1899827	0.93[ASN][1000 genomes]
rs2583992	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs312276	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4360771	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66578805	0.80[EUR][1000 genomes]
rs7300719	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7487913	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs932908	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs984129	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832379	chr12:41054440-41232749	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv832380	chr12:41132306-41323961	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3435443	chr12:41206734-41222972	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1126373	CPNE8	cis	parietal	SCAN
rs1126373	CNTN1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41214000-41218800	Weak transcription	A549	lung
2	chr12:41214000-41223200	Weak transcription	NHEK	skin
3	chr12:41214200-41220200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:41214200-41221400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:41214200-41221600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:41214400-41220600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:41214400-41221600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:41214600-41218800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:41215200-41218800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:41217400-41221400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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