Variant report

Variant	rs10817160
Chromosome Location	chr9:99898794-99898795
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10817135	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10980597	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10980622	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10980777	0.84[AMR][1000 genomes]
rs10980809	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11787964	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11794654	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12550854	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13283681	0.89[CEU][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13290939	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13292867	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13295383	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13297375	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13299950	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13301185	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13302714	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2001382	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34533733	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545208	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4573384	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4645657	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7032933	0.91[AMR][1000 genomes];0.88[EUR][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	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv972432	chr9:99874607-99958095	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv973382	chr9:99894731-99916071	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	lncRNA	n/a	inside rSNPs	diseases
4	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10817160	PTCH1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99889400-99908200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:99894000-99898800	Weak transcription	Spleen	Spleen
3	chr9:99894400-99898800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:99894400-99900400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:99894600-99901400	Weak transcription	Pancreas	Pancrea
6	chr9:99895600-99901000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:99895800-99898800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:99895800-99900800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:99895800-99902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:99897200-99899800	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr9:99897800-99902600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:99897800-99907600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:99898000-99902200	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr9:99898400-99899200	Enhancers	Fetal Intestine Large	intestine
15	chr9:99898400-99908600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:99898600-99898800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr9:99898600-99899200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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