Variant report

Variant	rs16909981
Chromosome Location	chr9:98313032-98313033
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf102-6	chr9:98312137-98313122	NONHSAT133382

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10512247	0.83[EUR][1000 genomes]
rs10512249	0.83[CEU][hapmap]
rs16909898	0.83[CEU][hapmap]
rs16909902	0.84[CEU][hapmap]
rs16909923	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16909927	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16909930	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16909964	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16909967	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16909975	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16909978	0.87[EUR][1000 genomes]
rs2282040	0.83[CEU][hapmap]
rs28372466	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28469297	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28520360	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28682502	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28698544	0.84[AMR][1000 genomes]
rs57594450	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57594805	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57793730	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60529258	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61660304	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73529860	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73654566	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73654567	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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	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
rs16909981	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98311800-98315400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:98312800-98315200	Weak transcription	Pancreas	Pancrea
3	chr9:98313000-98313200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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