Variant report

Variant	rs10963545
Chromosome Location	chr9:18269232-18269233
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10756954	0.85[ASN][1000 genomes]
rs10810939	0.87[ASN][1000 genomes]
rs10810940	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810941	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10963541	0.83[ASN][1000 genomes]
rs10963546	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10963549	0.83[ASN][1000 genomes]
rs12684857	0.92[ASN][1000 genomes]
rs13286417	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2891124	0.82[ASN][1000 genomes]
rs35615840	0.83[ASN][1000 genomes]
rs6475207	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7039570	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7039917	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7847636	0.84[ASN][1000 genomes]
rs7852708	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7861151	0.84[ASN][1000 genomes]
rs7862346	0.89[ASN][1000 genomes]
rs7862683	0.92[ASN][1000 genomes]
rs7870639	0.87[AMR][1000 genomes];0.94[EUR][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	nsv1021605	chr9:18002205-18271109	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv892682	chr9:18166112-18272700	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv831522	chr9:18231982-18459492	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv2764161	chr9:18247433-18443060	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv892684	chr9:18261485-18401585	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10963545	PTPLAD2	cis	cerebellum	SCAN
rs10963545	IFNA14	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18265200-18270200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:18266200-18269400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:18267200-18269400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:18267400-18269400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:18268000-18269400	Enhancers	HUVEC	blood vessel
6	chr9:18268000-18269400	Enhancers	NHLF	lung
7	chr9:18268200-18269400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:18268200-18269400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:18268200-18269600	Enhancers	Osteobl	bone
10	chr9:18268200-18270200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:18268200-18270400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:18268400-18269400	Enhancers	NHEK	skin
13	chr9:18269000-18269800	Enhancers	HMEC	breast
14	chr9:18269200-18269400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:18269200-18269400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:18269200-18271000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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