Variant report

Variant	rs1234352
Chromosome Location	chr7:112225536-112225537
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1234346	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs1234348	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1234350	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1234351	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234383	0.85[ASN][1000 genomes]
rs1236840	0.81[ASN][1000 genomes]
rs1613412	0.83[ASN][1000 genomes]
rs1623536	0.85[ASN][1000 genomes]
rs1796502	0.82[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2079530	0.94[CEU][hapmap];0.94[CHB][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2097672	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2188547	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2860402	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28844	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2905278	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2905280	0.83[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2952678	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2952687	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2952688	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs4473967	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4518580	0.94[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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 target site	105 gene(s)	inside rSNPs	diseases
2	nsv889055	chr7:112174089-112353440	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1234352	LRRN3	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112222200-112226000	Weak transcription	Stomach Mucosa	stomach
2	chr7:112224800-112225600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:112225000-112226000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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