Variant report

Variant	rs9530490
Chromosome Location	chr13:76476437-76476438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11616744	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17659925	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17716507	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17716584	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1983816	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983817	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982226	1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs7982357	0.82[AMR][1000 genomes]
rs9530480	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9530486	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530487	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9530488	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9544061	0.81[GIH][hapmap]
rs9544064	1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs9544073	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9544074	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9544075	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9593136	1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs9593140	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9600565	1.00[JPT][hapmap]
rs9600566	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9600569	1.00[JPT][hapmap]
rs9600570	1.00[JPT][hapmap]
rs9600576	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs9600588	0.90[EUR][1000 genomes];1.00[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	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1054431	chr13:76460431-76885094	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv541837	chr13:76460431-76885094	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9530490	TBC1D4	cis	lymphoblastoid	seeQTL
rs9530490	LMO7	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76464600-76478200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:76466400-76477800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:76475400-76477400	Enhancers	Fetal Heart	heart
4	chr13:76475600-76476600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr13:76475800-76476800	Enhancers	HSMMtube	muscle
6	chr13:76475800-76477400	Enhancers	Psoas Muscle	Psoas
7	chr13:76476000-76477200	Enhancers	Stomach Smooth Muscle	stomach
8	chr13:76476000-76477400	Enhancers	Aorta	Aorta
9	chr13:76476200-76476600	Enhancers	Left Ventricle	heart
10	chr13:76476200-76477200	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr13:76476400-76481000	Weak transcription	Fetal Muscle Leg	muscle
12	chr13:76476400-76481000	Weak transcription	Fetal Stomach	stomach

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