Variant report

Variant	rs4405040
Chromosome Location	chr9:93177556-93177557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10465157	0.83[EUR][1000 genomes]
rs10465158	0.86[EUR][1000 genomes]
rs10465163	0.86[EUR][1000 genomes]
rs10512198	0.85[EUR][1000 genomes]
rs10761365	0.86[EUR][1000 genomes]
rs10761367	0.86[EUR][1000 genomes]
rs10761373	0.86[EUR][1000 genomes]
rs10821391	0.84[EUR][1000 genomes]
rs10821396	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10821397	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10821399	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821403	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10821416	0.86[EUR][1000 genomes]
rs10821417	0.86[EUR][1000 genomes]
rs10821418	0.86[EUR][1000 genomes]
rs10821419	0.85[EUR][1000 genomes]
rs10821420	0.86[EUR][1000 genomes]
rs10821421	0.86[EUR][1000 genomes]
rs10821422	0.86[EUR][1000 genomes]
rs10821423	0.86[EUR][1000 genomes]
rs10821424	0.86[EUR][1000 genomes]
rs10821425	0.86[EUR][1000 genomes]
rs10821426	0.86[EUR][1000 genomes]
rs10821427	0.86[EUR][1000 genomes]
rs10821429	0.86[EUR][1000 genomes]
rs10821434	0.86[EUR][1000 genomes]
rs10821435	0.87[EUR][1000 genomes]
rs10821443	0.86[EUR][1000 genomes]
rs10821444	0.86[EUR][1000 genomes]
rs10821445	0.86[EUR][1000 genomes]
rs10821448	0.84[EUR][1000 genomes]
rs10993461	0.82[EUR][1000 genomes]
rs10993468	0.86[EUR][1000 genomes]
rs10993469	0.86[EUR][1000 genomes]
rs10993470	0.86[EUR][1000 genomes]
rs12375952	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12377373	0.86[EUR][1000 genomes]
rs2114349	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2892055	0.86[EUR][1000 genomes]
rs3748185	0.86[EUR][1000 genomes]
rs3748186	0.86[EUR][1000 genomes]
rs3748187	0.86[EUR][1000 genomes]
rs4237223	0.86[EUR][1000 genomes]
rs4237224	0.86[EUR][1000 genomes]
rs4595251	0.86[EUR][1000 genomes]
rs4743985	0.86[EUR][1000 genomes]
rs4743986	0.86[EUR][1000 genomes]
rs4743987	0.87[EUR][1000 genomes]
rs4744373	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744385	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4744396	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4744413	0.85[EUR][1000 genomes]
rs4744414	0.86[EUR][1000 genomes]
rs4744415	0.86[EUR][1000 genomes]
rs4744416	0.86[EUR][1000 genomes]
rs4744417	0.86[EUR][1000 genomes]
rs4744418	0.86[EUR][1000 genomes]
rs4744439	0.86[EUR][1000 genomes]
rs6479595	0.86[EUR][1000 genomes]
rs7869492	0.84[EUR][1000 genomes]
rs7870764	0.84[EUR][1000 genomes]
rs883922	0.86[EUR][1000 genomes]
rs913619	0.86[EUR][1000 genomes]
rs913620	0.86[EUR][1000 genomes]
rs913621	0.86[EUR][1000 genomes]
rs913622	0.86[EUR][1000 genomes]
rs9332454	0.86[EUR][1000 genomes]
rs944901	0.86[EUR][1000 genomes]
rs944902	0.86[EUR][1000 genomes]
rs944903	0.86[EUR][1000 genomes]
rs944904	0.86[EUR][1000 genomes]
rs9650753	0.83[EUR][1000 genomes];0.80[ASN][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	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv482748	chr9:93123377-93279526	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3483705	chr9:93162382-93194535	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3483706	chr9:93162396-93194531	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4405040	RP11-389K14.3	cis	lung	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93171200-93180800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:93174400-93180800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:93175000-93177600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr9:93175000-93178000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr9:93175200-93178600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr9:93176000-93180800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:93176200-93181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:93177400-93178000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr9:93177400-93180600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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