Variant report

Variant	rs9686857
Chromosome Location	chr5:43723915-43723916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10050726	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10054514	0.91[AMR][1000 genomes]
rs10055374	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10058555	0.91[EUR][1000 genomes]
rs10059613	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10064711	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10066806	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10071683	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10073552	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10077972	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10079935	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461747	0.87[EUR][1000 genomes]
rs10462054	0.81[EUR][1000 genomes]
rs10462055	0.84[EUR][1000 genomes]
rs10462056	0.87[EUR][1000 genomes]
rs10462057	0.87[EUR][1000 genomes]
rs10472386	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12332274	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13159393	0.84[EUR][1000 genomes]
rs13163981	0.87[EUR][1000 genomes]
rs13165656	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13170672	0.87[EUR][1000 genomes]
rs13173498	0.87[EUR][1000 genomes]
rs13173726	0.84[EUR][1000 genomes]
rs13175037	0.84[EUR][1000 genomes]
rs13177579	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13178040	0.87[EUR][1000 genomes]
rs13178059	0.87[EUR][1000 genomes]
rs13179099	0.82[EUR][1000 genomes]
rs13181483	0.81[EUR][1000 genomes]
rs13183122	0.81[EUR][1000 genomes]
rs13183124	0.87[EUR][1000 genomes]
rs13183238	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13184712	0.87[EUR][1000 genomes]
rs13187695	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13189630	0.81[EUR][1000 genomes]
rs16873433	0.81[EUR][1000 genomes]
rs16873443	0.81[EUR][1000 genomes]
rs16873454	0.87[EUR][1000 genomes]
rs16873455	0.87[EUR][1000 genomes]
rs16873466	0.87[EUR][1000 genomes]
rs16873471	0.87[EUR][1000 genomes]
rs16873502	0.87[EUR][1000 genomes]
rs2303732	0.87[EUR][1000 genomes]
rs2303733	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28520030	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34003086	0.87[EUR][1000 genomes]
rs34028586	0.87[EUR][1000 genomes]
rs34079397	0.87[EUR][1000 genomes]
rs34132518	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34289650	0.87[EUR][1000 genomes]
rs34307136	0.81[EUR][1000 genomes]
rs34308364	0.81[EUR][1000 genomes]
rs34361701	0.87[EUR][1000 genomes]
rs34418470	0.81[AMR][1000 genomes]
rs34420640	0.87[EUR][1000 genomes]
rs34435369	0.87[EUR][1000 genomes]
rs34571724	0.87[EUR][1000 genomes]
rs34814715	0.87[EUR][1000 genomes]
rs34844158	0.87[EUR][1000 genomes]
rs34897533	0.87[EUR][1000 genomes]
rs34902970	0.87[EUR][1000 genomes]
rs34985223	0.81[EUR][1000 genomes]
rs35023717	0.81[EUR][1000 genomes]
rs35047682	0.87[EUR][1000 genomes]
rs35141665	0.87[EUR][1000 genomes]
rs35249562	0.87[EUR][1000 genomes]
rs35370110	0.87[EUR][1000 genomes]
rs35429460	0.85[EUR][1000 genomes]
rs35442919	0.87[EUR][1000 genomes]
rs35606071	0.87[EUR][1000 genomes]
rs35609488	0.87[EUR][1000 genomes]
rs35663171	0.87[EUR][1000 genomes]
rs35773128	0.87[EUR][1000 genomes]
rs35818459	0.87[EUR][1000 genomes]
rs35910245	0.81[EUR][1000 genomes]
rs35955731	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3792921	0.81[EUR][1000 genomes]
rs3792922	0.81[EUR][1000 genomes]
rs3805720	0.81[EUR][1000 genomes]
rs3805721	0.81[EUR][1000 genomes]
rs3805723	0.81[EUR][1000 genomes]
rs3828695	0.81[EUR][1000 genomes]
rs3828696	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41271083	0.81[EUR][1000 genomes]
rs4380668	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4382179	0.87[EUR][1000 genomes]
rs4476731	0.84[EUR][1000 genomes]
rs62367633	0.81[EUR][1000 genomes]
rs62367649	0.81[EUR][1000 genomes]
rs62367651	0.81[EUR][1000 genomes]
rs62367653	0.87[EUR][1000 genomes]
rs62367658	0.87[EUR][1000 genomes]
rs62368561	0.87[EUR][1000 genomes]
rs62368564	0.87[EUR][1000 genomes]
rs62368567	0.87[EUR][1000 genomes]
rs62368570	0.84[EUR][1000 genomes]
rs62368571	0.87[EUR][1000 genomes]
rs62368574	0.87[EUR][1000 genomes]
rs62368575	0.87[EUR][1000 genomes]
rs62368577	0.87[EUR][1000 genomes]
rs62368578	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62368581	0.87[EUR][1000 genomes]
rs62368584	0.87[EUR][1000 genomes]
rs62368636	0.87[EUR][1000 genomes]
rs62368637	0.87[EUR][1000 genomes]
rs62368641	0.87[EUR][1000 genomes]
rs62368656	0.84[EUR][1000 genomes]
rs62369476	0.87[EUR][1000 genomes]
rs62369480	0.87[EUR][1000 genomes]
rs62369481	0.84[EUR][1000 genomes]
rs6862487	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6878821	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6895383	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71629184	0.81[EUR][1000 genomes]
rs71629187	0.87[EUR][1000 genomes]
rs71629189	0.87[EUR][1000 genomes]
rs71629192	0.97[EUR][1000 genomes]
rs71629193	0.87[EUR][1000 genomes]
rs716960	0.87[EUR][1000 genomes]
rs7708386	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7711370	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7733259	0.91[AMR][1000 genomes];0.97[EUR][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	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv3471542	chr5:43665651-43824536	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv3471543	chr5:43665767-43824443	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9686857	RP11-159F24.1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43706000-43725000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:43723600-43726200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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