Variant report

Variant	rs10024198
Chromosome Location	chr4:95060602-95060603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10008044	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10018905	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10023115	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10023582	0.81[EUR][1000 genomes]
rs10433969	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516947	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11943926	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12501138	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12505596	0.80[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12505694	0.83[EUR][1000 genomes]
rs12513267	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1472984	0.82[EUR][1000 genomes]
rs1509945	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1509946	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1585651	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17302300	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17374832	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1876918	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2171384	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2632412	0.83[JPT][hapmap]
rs28408270	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28469860	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2865343	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2865344	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34396894	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4438731	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4560373	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4692999	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4693368	0.83[EUR][1000 genomes]
rs4693374	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4693375	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5019896	0.81[EUR][1000 genomes]
rs6532469	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6532472	0.80[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6815207	0.89[EUR][1000 genomes]
rs6817795	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6821438	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6821638	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6857967	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6858265	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6858342	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs722486	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72665608	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72665629	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7340895	0.80[ASN][1000 genomes]
rs7437089	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7654565	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7654919	0.80[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7668980	0.82[EUR][1000 genomes]
rs7669168	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7676797	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7678054	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7680953	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8336	0.84[MKK][hapmap]
rs9307136	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9307137	0.90[EUR][1000 genomes]
rs965807	0.83[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	nsv931979	chr4:94289958-95121723	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv821636	chr4:94439636-95116590	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv879618	chr4:94980768-95136164	Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv879621	chr4:95046907-95099194	Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10024198	ATOH1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95052200-95061400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:95056400-95063400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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