Variant report

Variant	rs672392
Chromosome Location	chr11:94028887-94028888
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11020719	0.81[EUR][1000 genomes]
rs1257950	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12803129	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1361929	0.85[EUR][1000 genomes]
rs1541299	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1541301	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs16920039	0.81[CEU][hapmap]
rs1789652	0.81[CEU][hapmap]
rs1833063	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2051464	0.96[EUR][1000 genomes]
rs3020004	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs3020016	0.92[CEU][hapmap]
rs4753548	0.81[AMR][1000 genomes]
rs4753569	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs519834	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526036	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs528327	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs532037	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs545450	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs552267	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556758	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561807	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs579574	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs581123	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs584109	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs603157	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6483324	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs655358	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs656810	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs657242	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657896	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs669634	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs688910	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7115129	0.85[EUR][1000 genomes]
rs7130456	0.84[EUR][1000 genomes]
rs7944234	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs871244	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	nsv523083	chr11:93962121-94150790	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832233	chr11:93981434-94158471	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs672392	PANX1	cis	parietal	SCAN
rs672392	GPR83	cis	cerebellum	SCAN
rs672392	JRKL	cis	cerebellum	SCAN
rs672392	MRE11A	cis	parietal	SCAN
rs672392	GPR83	cis	parietal	SCAN
rs672392	PANX1	cis	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:94026600-94030600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:94028200-94029000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:94028600-94029000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:94028600-94029200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr11:94028600-94029400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:94028600-94029800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:94028800-94029200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:94028800-94029600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:94028800-94029800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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