Variant report

Variant	rs17079862
Chromosome Location	chr6:118552454-118552455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11153725	0.84[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12202829	0.84[AMR][1000 genomes]
rs176014	0.91[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes]
rs1874082	0.81[EUR][1000 genomes]
rs190756	0.89[CHB][hapmap]
rs1923282	0.91[CEU][hapmap];0.88[CHB][hapmap]
rs205915	0.84[AMR][1000 genomes]
rs205916	0.84[AMR][1000 genomes]
rs2105020	0.84[AMR][1000 genomes]
rs2356077	0.84[AMR][1000 genomes]
rs281866	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs281869	0.95[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs281872	0.91[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs283067	0.87[EUR][1000 genomes]
rs283083	0.91[CEU][hapmap];0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs2883849	0.95[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs387266	0.87[EUR][1000 genomes]
rs413876	0.95[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs427027	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs450093	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes]
rs4945618	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58826473	0.81[AMR][1000 genomes]
rs9320646	0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9385038	0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9387565	0.84[AMR][1000 genomes]
rs9398485	0.84[AMR][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	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv428153	chr6:118430517-118586974	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1030089	chr6:118436482-118604516	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538427	chr6:118436482-118604516	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118546400-118564000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:118551600-118553200	Enhancers	Cortex derived primary cultured neurospheres	brain

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