Variant report

Variant	rs3927680
Chromosome Location	chr9:16887366-16887367
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10756822	1.00[ASN][1000 genomes]
rs10810650	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10810652	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810655	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810657	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10810658	0.94[ASN][1000 genomes]
rs10962650	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10962668	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10962674	0.93[ASN][1000 genomes]
rs12338590	0.90[ASN][1000 genomes]
rs12345776	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12350739	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1339552	0.92[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1416742	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1890640	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2153271	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28498684	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36116821	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4644350	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62541919	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7040151	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
2	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892652	chr9:16843128-16958312	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	nsv892653	chr9:16848790-16895610	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	nsv1018615	chr9:16865804-16960970	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	nsv540074	chr9:16865804-16960970	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3927680	CNTLN	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16886200-16887600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:16886200-16888000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr9:16886400-16887400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:16886400-16887600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:16886800-16888000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:16887000-16887800	Enhancers	Dnd41	blood
7	chr9:16887200-16887400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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