Variant report

Variant	rs1269602
Chromosome Location	chr10:116941272-116941273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116940963..116942966-chr10:116944377..116947212,2	MCF-7	breast:
2	chr10:116931808..116934007-chr10:116939666..116942604,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10787554	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10787555	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10787557	0.80[EUR][1000 genomes]
rs10787558	0.85[EUR][1000 genomes]
rs10885649	0.81[EUR][1000 genomes]
rs10885651	0.88[EUR][1000 genomes]
rs10885655	0.89[EUR][1000 genomes]
rs10885657	0.82[EUR][1000 genomes]
rs10885658	0.92[EUR][1000 genomes]
rs10885659	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10885660	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10885662	0.91[EUR][1000 genomes]
rs10885664	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10885669	0.95[EUR][1000 genomes]
rs10885671	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10885672	0.94[EUR][1000 genomes]
rs10885673	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10885675	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10885676	0.93[EUR][1000 genomes]
rs10885677	0.91[EUR][1000 genomes]
rs10885680	0.88[EUR][1000 genomes]
rs10885681	0.89[EUR][1000 genomes]
rs10885682	0.84[EUR][1000 genomes]
rs10885683	0.88[EUR][1000 genomes]
rs11197066	0.86[EUR][1000 genomes]
rs11197071	0.86[EUR][1000 genomes]
rs11197081	0.91[EUR][1000 genomes]
rs11197084	0.94[EUR][1000 genomes]
rs11197087	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11197091	0.91[EUR][1000 genomes]
rs11197093	0.92[ASN][1000 genomes]
rs11197094	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11197103	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11197107	0.96[EUR][1000 genomes]
rs11197110	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11197122	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11197126	0.97[EUR][1000 genomes]
rs11197127	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11197139	0.94[EUR][1000 genomes]
rs11197149	0.85[EUR][1000 genomes]
rs11197150	0.85[EUR][1000 genomes]
rs11197159	0.88[EUR][1000 genomes]
rs11197160	0.83[EUR][1000 genomes]
rs11197168	0.83[EUR][1000 genomes]
rs11517121	0.84[EUR][1000 genomes]
rs11525277	0.89[EUR][1000 genomes]
rs11527959	0.80[EUR][1000 genomes]
rs12218100	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12218477	0.83[EUR][1000 genomes]
rs12355617	0.89[EUR][1000 genomes]
rs12357053	0.85[EUR][1000 genomes]
rs12358411	0.94[EUR][1000 genomes]
rs12360503	0.94[EUR][1000 genomes]
rs12573443	0.96[EUR][1000 genomes]
rs1264748	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1264756	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1264763	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1264765	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1264768	0.85[EUR][1000 genomes]
rs1264794	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1264795	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1264796	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1264802	0.89[EUR][1000 genomes]
rs1268459	0.81[ASN][1000 genomes]
rs1268460	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1268916	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1270442	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1537685	0.91[EUR][1000 genomes]
rs17092908	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17722681	0.92[EUR][1000 genomes]
rs1899718	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1899721	0.99[EUR][1000 genomes]
rs2050705	0.80[EUR][1000 genomes]
rs2152148	0.89[EUR][1000 genomes]
rs2172669	0.88[EUR][1000 genomes]
rs2256046	0.93[EUR][1000 genomes]
rs2265930	0.82[EUR][1000 genomes]
rs2420075	0.91[EUR][1000 genomes]
rs2420077	0.85[EUR][1000 genomes]
rs2420078	0.82[EUR][1000 genomes]
rs2440313	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2492980	0.81[EUR][1000 genomes]
rs2492981	0.84[EUR][1000 genomes]
rs34938864	0.83[EUR][1000 genomes]
rs35120367	0.90[EUR][1000 genomes]
rs35728982	0.89[EUR][1000 genomes]
rs4752724	0.95[EUR][1000 genomes]
rs61880825	0.88[EUR][1000 genomes]
rs7474585	0.98[EUR][1000 genomes]
rs7912050	0.80[EUR][1000 genomes]
rs923907	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3424905	chr10:116941162-116945560	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1269602	ATRNL1	cis	Muscle Skeletal	GTEx
rs1269602	ATRNL1	cis	Esophagus Muscularis	GTEx

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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