Variant report

Variant	rs10759522
Chromosome Location	chr9:99981972-99981973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10116019	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10119245	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817265	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981209	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10981280	0.81[EUR][1000 genomes]
rs10981288	0.81[EUR][1000 genomes]
rs10981296	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11562326	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11794422	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11998999	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12235734	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13297670	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13299029	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28846196	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3957904	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994556	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4626726	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55694850	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6478020	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7022475	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7039446	0.86[ASN][1000 genomes]
rs7850392	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7850429	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7850504	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7855366	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7855622	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7868440	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7868563	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7868806	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7869509	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7869568	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7869587	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7869959	0.94[AMR][1000 genomes];0.85[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	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
4	nsv972433	chr9:99962059-99983443	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10759522	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs10759522	VN1R51P	cis	Thyroid	GTEx
rs10759522	ANKRD18CP	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99976200-99983000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:99976600-99985000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr9:99976600-99985000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr9:99976800-99985200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr9:99976800-99985400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr9:99979600-99982000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:99979600-99982400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:99980000-99983000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:99980800-99982200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr9:99981400-99985000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr9:99981800-99982000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr9:99981800-99985000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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