Variant report

Variant	rs9327450
Chromosome Location	chr5:127098999-127099000
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10051341	0.81[EUR][1000 genomes]
rs10054323	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10066599	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10079426	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1228885	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13182486	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13188453	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432640	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654087	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1710276	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248694	0.96[CEU][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.98[TSI][hapmap]
rs248705	0.96[CEU][hapmap]
rs248707	0.92[CEU][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs248725	0.96[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs248727	0.89[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
rs248728	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248729	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248734	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34347180	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36138701	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36170620	0.80[EUR][1000 genomes]
rs4835930	0.96[EUR][1000 genomes]
rs7731022	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790832	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs790833	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs790835	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs790837	0.92[CEU][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs813165	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830480	chr5:126964751-127124522	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9327450	CTXN3	cis	parietal	SCAN
rs9327450	SLC12A2	cis	cerebellum	SCAN
rs9327450	FBN2	cis	brain	BrainEAC
rs9327450	FBN2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127090800-127102400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:127094000-127101800	Weak transcription	HUVEC	blood vessel
3	chr5:127095200-127102800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:127096400-127099800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:127096600-127099000	Enhancers	Brain Hippocampus Middle	brain
6	chr5:127096600-127099000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr5:127098000-127099200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:127098200-127099000	Enhancers	Brain Anterior Caudate	brain
9	chr5:127098200-127099000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr5:127098200-127099000	Enhancers	Right Atrium	heart
11	chr5:127098600-127099200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:127098600-127102800	Weak transcription	Psoas Muscle	Psoas
13	chr5:127098800-127099000	Enhancers	Left Ventricle	heart
14	chr5:127098800-127099200	Enhancers	Brain Substantia Nigra	brain

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