Variant report

Variant	rs16909978
Chromosome Location	chr9:98307990-98307991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98307185..98309730-chr9:98321412..98323508,2	K562	blood:
2	chr9:98292772..98295168-chr9:98307329..98310025,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10512247	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10512249	0.82[CEU][hapmap]
rs16909898	0.82[CEU][hapmap]
rs16909902	0.83[CEU][hapmap]
rs16909922	0.82[ASN][1000 genomes]
rs16909923	0.89[EUR][1000 genomes]
rs16909927	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs16909930	0.89[EUR][1000 genomes]
rs16909964	0.88[EUR][1000 genomes]
rs16909967	0.93[EUR][1000 genomes]
rs16909975	0.98[EUR][1000 genomes]
rs16909981	0.87[EUR][1000 genomes]
rs2282040	0.82[CEU][hapmap]
rs2282043	0.91[CEU][hapmap]
rs28372466	0.89[EUR][1000 genomes]
rs28427480	0.82[ASN][1000 genomes]
rs28446321	0.80[ASN][1000 genomes]
rs28469297	0.84[CEU][hapmap]
rs28520360	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs28682502	0.89[EUR][1000 genomes]
rs28698544	0.87[EUR][1000 genomes]
rs3824488	0.91[CEU][hapmap]
rs57594450	0.89[EUR][1000 genomes]
rs57594805	0.89[EUR][1000 genomes]
rs57793730	0.90[EUR][1000 genomes]
rs60150206	0.82[ASN][1000 genomes]
rs60417486	0.82[ASN][1000 genomes]
rs60529258	0.98[EUR][1000 genomes]
rs61076166	0.87[EUR][1000 genomes]
rs61660304	0.95[EUR][1000 genomes]
rs73529860	0.83[EUR][1000 genomes]
rs73654566	0.98[EUR][1000 genomes]
rs73654567	0.96[EUR][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	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16909978	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98307600-98309000	Enhancers	Fetal Lung	lung
2	chr9:98307800-98308800	Enhancers	Cortex derived primary cultured neurospheres	brain

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