Variant report

Variant	rs16936492
Chromosome Location	chr9:18268661-18268662
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10116041	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10124717	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10810942	0.82[AMR][1000 genomes]
rs10963542	0.87[AMR][1000 genomes]
rs10963551	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2809854	0.94[ASN][1000 genomes]
rs2891125	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62548565	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62548566	0.84[AFR][1000 genomes];0.99[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16936492	IFNA2	cis	cerebellum	SCAN
rs16936492	MLLT3	cis	parietal	SCAN
rs16936492	BIN3	trans	parietal	SCAN
rs16936492	IFNA13	cis	parietal	SCAN
rs16936492	CDKN2B	cis	cerebellum	SCAN

Chromatin state (count:25 , 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	chr9:18267200-18269000	Enhancers	NHDF-Ad	bronchial
4	chr9:18267200-18269400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:18267400-18269400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:18267800-18269000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr9:18268000-18268800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:18268000-18269000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr9:18268000-18269000	Enhancers	HSMM	muscle
10	chr9:18268000-18269400	Enhancers	HUVEC	blood vessel
11	chr9:18268000-18269400	Enhancers	NHLF	lung
12	chr9:18268200-18269000	Enhancers	NH-A	brain
13	chr9:18268200-18269200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:18268200-18269400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:18268200-18269400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:18268200-18269600	Enhancers	Osteobl	bone
17	chr9:18268200-18270200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:18268200-18270400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:18268400-18268800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:18268400-18268800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr9:18268400-18268800	Enhancers	HSMMtube	muscle
22	chr9:18268400-18269200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:18268400-18269200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:18268400-18269400	Enhancers	NHEK	skin
25	chr9:18268600-18269000	Weak transcription	HMEC	breast

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