Variant report

Variant	rs11790079
Chromosome Location	chr9:73884985-73884986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10081739	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10429567	0.92[ASN][1000 genomes]
rs10746867	0.96[ASN][1000 genomes]
rs10781007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868993	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10868994	0.96[ASN][1000 genomes]
rs10869009	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11142749	0.96[ASN][1000 genomes]
rs11142764	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142775	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11142776	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12340517	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12340836	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12344426	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12346966	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12551732	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1394305	0.86[ASN][1000 genomes]
rs1504381	0.92[ASN][1000 genomes]
rs1504382	0.87[ASN][1000 genomes]
rs1504398	0.88[ASN][1000 genomes]
rs1580913	0.96[ASN][1000 genomes]
rs17056652	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1818186	0.90[ASN][1000 genomes]
rs2134858	0.88[ASN][1000 genomes]
rs2309909	0.96[ASN][1000 genomes]
rs4744626	0.95[ASN][1000 genomes]
rs4744627	0.96[ASN][1000 genomes]
rs4745072	0.90[ASN][1000 genomes]
rs4745077	0.96[ASN][1000 genomes]
rs62543438	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7020698	0.92[ASN][1000 genomes]
rs7022575	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7038340	0.96[ASN][1000 genomes]
rs7039499	0.96[ASN][1000 genomes]
rs7044340	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs716387	0.87[ASN][1000 genomes]
rs7850256	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7857188	0.96[ASN][1000 genomes]
rs7858061	0.92[ASN][1000 genomes]
rs7860940	0.92[ASN][1000 genomes]
rs7863093	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7865091	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7865847	0.80[ASN][1000 genomes]
rs7873142	0.96[ASN][1000 genomes]
rs9785223	0.96[ASN][1000 genomes]
rs989923	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035505	chr9:73709852-73934353	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv893442	chr9:73778502-74115344	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1052375	chr9:73793681-73893133	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv540152	chr9:73793681-73893133	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv893443	chr9:73859086-74008905	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv916062	chr9:73861614-74246247	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11790079	FAM108B1	cis	parietal	SCAN
rs11790079	DDX59	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73882200-73887600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:73884000-73885000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:73884000-73887600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:73884400-73887200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:73884800-73886600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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