Variant report

Variant	rs1270442
Chromosome Location	chr10:116948174-116948175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1010610	0.85[EUR][1000 genomes]
rs10736240	0.88[ASW][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs10787554	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10787555	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10787557	0.89[CEU][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs10885658	0.84[ASN][1000 genomes]
rs10885659	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10885660	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10885661	0.83[EUR][1000 genomes]
rs10885662	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs10885664	0.81[CEU][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10885669	0.81[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs10885671	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10885672	0.81[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs10885673	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10885675	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs10885676	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs10885677	0.82[EUR][1000 genomes]
rs10885680	0.82[JPT][hapmap]
rs10885681	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs10885683	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs10885692	0.82[JPT][hapmap]
rs10885696	0.85[CEU][hapmap]
rs11197072	0.82[JPT][hapmap];0.82[TSI][hapmap]
rs11197081	0.82[ASN][1000 genomes]
rs11197084	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs11197087	0.87[ASN][1000 genomes]
rs11197091	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs11197093	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11197094	0.85[ASN][1000 genomes]
rs11197103	0.86[EUR][1000 genomes]
rs11197107	0.80[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs11197110	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11197115	0.82[JPT][hapmap]
rs11197122	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11197127	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11197150	0.81[JPT][hapmap]
rs11197162	0.81[CEU][hapmap]
rs11197163	0.82[JPT][hapmap]
rs11197165	0.81[CEU][hapmap]
rs11197167	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs11197168	0.82[JPT][hapmap]
rs12218100	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12254019	0.85[CEU][hapmap]
rs12357053	0.82[JPT][hapmap]
rs12358411	0.81[JPT][hapmap]
rs12573443	0.84[CEU][hapmap]
rs1264748	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264756	0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1264763	1.00[ASW][hapmap];0.89[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1264765	0.91[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1264768	0.88[CEU][hapmap];0.80[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1264774	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1264776	0.83[YRI][hapmap]
rs1264782	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1264783	0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs1264794	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs1264795	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1264796	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1264799	0.85[EUR][1000 genomes]
rs1268459	0.85[EUR][1000 genomes]
rs1268460	0.88[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1268916	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1269602	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1270654	0.85[EUR][1000 genomes]
rs1389647	0.81[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs1537685	0.81[CEU][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1663157	0.89[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs17092908	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17722681	0.81[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs1899718	0.83[ASN][1000 genomes]
rs1899721	0.81[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2256046	0.81[CEU][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs2265930	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2440313	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2492980	0.88[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs2492981	0.89[EUR][1000 genomes]
rs35120367	0.81[EUR][1000 genomes]
rs4752724	0.81[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs7474585	0.81[EUR][1000 genomes]
rs923907	0.82[JPT][hapmap]

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	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv831998	chr10:116847998-116969618	Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv869279	chr10:116884639-117032437	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv868940	chr10:116933802-117032437	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1270442	ATRNL1	cis	Esophagus Muscularis	GTEx
rs1270442	ATRNL1	cis	parietal	SCAN
rs1270442	ATRNL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116926600-116951400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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