Variant report

Variant	rs11159408
Chromosome Location	chr14:79874358-79874359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10450934	0.81[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10450935	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873322	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11622878	0.86[AMR][1000 genomes]
rs11625634	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12888219	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12888940	0.82[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17109094	1.00[YRI][hapmap]
rs17109102	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs17758133	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1984716	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1993009	0.87[CEU][hapmap];0.92[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1993010	0.89[YRI][hapmap]
rs1993011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1993012	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2164434	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2164435	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2167150	0.90[YRI][hapmap]
rs2196444	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2196446	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2197988	0.83[TSI][hapmap]
rs2217887	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2218782	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2574750	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2574751	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2574752	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2597086	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2597087	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2597089	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2597091	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2597092	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34094616	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34848585	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35820490	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4603484	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs61993113	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61993118	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs714276	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs954860	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][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	nsv931412	chr14:79420297-79928269	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv902110	chr14:79624492-79998294	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv530072	chr14:79769657-79928269	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv902111	chr14:79807197-79890677	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11159408	ISCA2	cis	cerebellum	SCAN
rs11159408	C14orf145	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79861800-79874600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr14:79867800-79877600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr14:79872600-79884800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr14:79872800-79874400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr14:79873200-79875200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr14:79873800-79874600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr14:79873800-79875800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr14:79873800-79875800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr14:79874000-79874400	Enhancers	NHEK	skin
10	chr14:79874000-79874600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:79874000-79875800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr14:79874200-79877800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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