Variant report

Variant	rs17062428
Chromosome Location	chr9:78928711-78928712
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10115887	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10115893	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10119293	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1078866	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1078867	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11144826	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12336000	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17721158	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2257718	0.82[EUR][1000 genomes]
rs6560511	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7022994	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7023121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7043376	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv508552	chr9:78864913-78956326	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv893477	chr9:78892526-78932928	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17062428	PCA3	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78913400-78935200	Weak transcription	Small Intestine	intestine
2	chr9:78922600-78953400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:78927200-78930800	Weak transcription	Fetal Intestine Large	intestine
4	chr9:78927400-78929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:78927400-78930200	Weak transcription	Placenta	Placenta
6	chr9:78927800-78929000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr9:78927800-78929200	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr9:78927800-78929400	Enhancers	Stomach Mucosa	stomach
9	chr9:78928200-78929800	Genic enhancers	Fetal Intestine Small	intestine
10	chr9:78928400-78929000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr9:78928600-78928800	Enhancers	Colonic Mucosa	Colon
12	chr9:78928600-78931400	Enhancers	Placenta Amnion	Placenta Amnion

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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