Variant report

Variant	rs13297670
Chromosome Location	chr9:99990565-99990566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10116019	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10119245	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10759522	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10817265	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10981209	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10981280	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981288	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981296	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981329	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981438	0.83[EUR][1000 genomes]
rs11562326	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11791310	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11794422	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11998999	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004930	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12005128	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12235305	0.83[EUR][1000 genomes]
rs12235734	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13298346	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13299627	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13301357	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13302699	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1544203	0.83[EUR][1000 genomes]
rs1857083	0.85[AMR][1000 genomes]
rs1903635	0.82[EUR][1000 genomes]
rs2219664	0.82[EUR][1000 genomes]
rs2374923	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2493442	0.82[EUR][1000 genomes]
rs2493443	0.82[EUR][1000 genomes]
rs2502644	0.82[EUR][1000 genomes]
rs2615143	0.82[EUR][1000 genomes]
rs2615145	0.82[EUR][1000 genomes]
rs2795365	0.82[EUR][1000 genomes]
rs2795367	0.83[EUR][1000 genomes]
rs2818238	0.82[EUR][1000 genomes]
rs2818239	0.82[EUR][1000 genomes]
rs2818243	0.82[EUR][1000 genomes]
rs28846196	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3214072	0.82[EUR][1000 genomes]
rs34382632	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34955252	0.82[EUR][1000 genomes]
rs35609998	0.83[EUR][1000 genomes]
rs3957904	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3994556	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4014789	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4284138	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4452918	0.81[AMR][1000 genomes]
rs4523384	0.83[EUR][1000 genomes]
rs4626726	0.93[EUR][1000 genomes]
rs55694850	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62556614	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6478020	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7022475	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs713066	0.82[EUR][1000 genomes]
rs72747776	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7470446	0.82[EUR][1000 genomes]
rs7850392	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7850504	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7855366	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7855622	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7868440	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7868563	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7868806	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7869509	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7869568	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7869587	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7869959	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13297670	VN1R51P	cis	Thyroid	GTEx
rs13297670	ANKRD18CP	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99985200-99992000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:99985200-99995000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:99985800-99994800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:99986600-99994200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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