Variant report

Variant	rs4753116
Chromosome Location	chr11:93767360-93767361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1401182	0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1401183	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1518562	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2460045	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2460054	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2460055	0.83[GIH][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2511386	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2511401	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2511402	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4084250	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4753117	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4753118	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4753120	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4753530	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5002769	0.88[CHD][hapmap]
rs949452	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][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	nsv1049467	chr11:93651025-93778717	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv898183	chr11:93725384-93906735	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv898184	chr11:93741612-93969726	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4753116	PANX1	cis	cerebellum	SCAN
rs4753116	GPR83	cis	cerebellum	SCAN
rs4753116	AMOTL1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93763200-93767400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:93763600-93767400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:93766800-93768400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:93767000-93768200	Enhancers	HMEC	breast
5	chr11:93767000-93768400	Enhancers	NHEK	skin
6	chr11:93767200-93768000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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