Variant report

Variant	rs11789634
Chromosome Location	chr9:104673545-104673546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1072843	0.84[ASN][1000 genomes]
rs1072844	0.82[ASN][1000 genomes]
rs10989694	0.84[ASN][1000 genomes]
rs10989695	0.84[ASN][1000 genomes]
rs12335958	0.86[ASN][1000 genomes]
rs12337741	0.84[ASN][1000 genomes]
rs12343857	0.86[ASN][1000 genomes]
rs12349971	0.86[ASN][1000 genomes]
rs1555461	0.84[ASN][1000 genomes]
rs1555463	0.84[ASN][1000 genomes]
rs1555464	0.84[ASN][1000 genomes]
rs2224531	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479070	0.83[ASN][1000 genomes]
rs6479071	0.83[ASN][1000 genomes]
rs7019893	0.87[ASN][1000 genomes]
rs7022010	0.86[ASN][1000 genomes]
rs7037678	0.83[ASN][1000 genomes]
rs7042948	0.86[ASN][1000 genomes]
rs73508878	0.80[ASN][1000 genomes]
rs7852867	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046590	chr9:104450624-104848588	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1046614	chr9:104492314-104686326	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1054992	chr9:104494816-104771134	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1048227	chr9:104546761-105162810	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893631	chr9:104566472-104673545	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1045195	chr9:104611014-104805388	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv540181	chr9:104611014-104805388	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv2757345	chr9:104637950-104782713	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv2759704	chr9:104637950-104825559	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv2758195	chr9:104640232-104825559	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv893632	chr9:104642966-104739780	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv893633	chr9:104642966-104902874	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv521116	chr9:104642966-104904454	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11789634	SMC2	cis	parietal	SCAN
rs11789634	NR4A3	cis	parietal	SCAN
rs11789634	SEC61B	cis	cerebellum	SCAN
rs11789634	NCBP1	cis	cerebellum	SCAN
rs11789634	SMC2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104669600-104674800	Weak transcription	Adipose Nuclei	Adipose
2	chr9:104673000-104673800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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