Variant report

Variant	rs17826509
Chromosome Location	chr16:80748868-80748869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11643615	0.86[AFR][1000 genomes]
rs11648230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17761499	0.82[ASW][hapmap]
rs2316576	0.88[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34405003	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4497705	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56338398	0.86[AFR][1000 genomes]
rs56364344	0.86[AFR][1000 genomes]
rs7200532	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72807926	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7498627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8046061	1.00[LWK][hapmap];0.86[AFR][1000 genomes]
rs8047401	0.88[CEU][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1057357	chr16:80662770-80794945	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3451298	chr16:80696935-80997389	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3350075	chr16:80696955-80997359	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542990	chr16:80729797-80918198	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv833301	chr16:80732170-80928751	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17826509	PKD1L2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80689000-80751000	Weak transcription	Pancreas	Pancrea
2	chr16:80738400-80751800	Weak transcription	Gastric	stomach
3	chr16:80742200-80751800	Weak transcription	HUVEC	blood vessel
4	chr16:80744000-80753400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr16:80745200-80753400	Weak transcription	Primary T cells from cord blood	blood
6	chr16:80747000-80751800	Weak transcription	Spleen	Spleen
7	chr16:80747400-80749000	ZNF genes & repeats	Fetal Intestine Small	intestine
8	chr16:80748400-80750400	Strong transcription	Hela-S3	cervix

Quick Search:

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

what's new

Quick links