Variant report

Variant	rs16909927
Chromosome Location	chr9:98284175-98284176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr9:98284051-98284315	Hela-S3	cervix:	n/a	chr9:98284173-98284182 chr9:98284172-98284183 chr9:98284171-98284184 chr9:98284172-98284181 chr9:98284173-98284182 chr9:98284167-98284188
2	USF2	chr9:98284018-98284315	HepG2	liver:	n/a	chr9:98284173-98284182 chr9:98284172-98284183 chr9:98284171-98284184 chr9:98284172-98284181 chr9:98284173-98284182 chr9:98284167-98284188
3	USF1	chr9:98283997-98284295	K562	blood:	n/a	chr9:98284173-98284182 chr9:98284171-98284184 chr9:98284172-98284181 chr9:98284173-98284182 chr9:98284167-98284188

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98277913..98281548-chr9:98282175..98286855,6	K562	blood:
2	chr9:98276379..98279756-chr9:98281415..98285056,4	MCF-7	breast:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10512247	0.94[EUR][1000 genomes]
rs10512249	0.84[CEU][hapmap]
rs16909898	0.84[CEU][hapmap]
rs16909902	0.84[CEU][hapmap]
rs16909923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909933	0.83[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs16909938	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs16909952	0.90[AFR][1000 genomes]
rs16909953	0.90[AFR][1000 genomes]
rs16909955	0.90[AFR][1000 genomes]
rs16909958	0.86[AFR][1000 genomes]
rs16909964	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909975	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16909978	0.89[EUR][1000 genomes]
rs16909981	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2282040	0.84[CEU][hapmap]
rs2405050	0.90[AFR][1000 genomes]
rs28372466	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28377534	0.82[AFR][1000 genomes]
rs28428695	0.94[AFR][1000 genomes]
rs28453815	0.84[AFR][1000 genomes]
rs28469297	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs28520360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28536770	0.97[AFR][1000 genomes]
rs28540597	0.97[AFR][1000 genomes]
rs28555445	0.97[AFR][1000 genomes]
rs28645521	0.97[AFR][1000 genomes]
rs28682502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28698544	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28719604	0.97[AFR][1000 genomes]
rs28731018	0.97[AFR][1000 genomes]
rs28778940	0.82[AFR][1000 genomes]
rs3847313	0.90[AFR][1000 genomes]
rs3858091	0.87[AFR][1000 genomes]
rs3858093	0.90[AFR][1000 genomes]
rs57594450	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57594805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57686793	0.91[AFR][1000 genomes]
rs57735870	0.90[AFR][1000 genomes]
rs57793730	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59139263	0.89[AFR][1000 genomes]
rs59208894	0.90[AFR][1000 genomes]
rs59836541	0.91[AFR][1000 genomes]
rs60529258	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60984818	0.84[AFR][1000 genomes]
rs61076166	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61128152	0.95[AFR][1000 genomes]
rs61548355	0.94[AFR][1000 genomes]
rs61660304	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73529860	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73654566	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73654567	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[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	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
6	nsv917118	chr9:98279162-98284265	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16909927	PTCH1	Cis_1M	lymphoblastoid	RTeQTL
rs16909927	FBP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98283600-98285200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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