Variant report

Variant	rs2462753
Chromosome Location	chr11:93781312-93781313
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10765649	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10765650	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10765651	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10831160	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10831161	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10831162	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11020641	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11020642	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11020645	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12420636	0.86[EUR][1000 genomes]
rs1401181	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1878800	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1894167	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1945784	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1961012	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1984373	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2032399	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2252036	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2460042	0.89[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2460063	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2511378	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2511379	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2511406	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4753122	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4753531	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4753532	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4753534	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5002769	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7110588	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7127348	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7938136	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7945945	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7946162	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs982543	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs982544	0.84[AMR][1000 genomes];0.93[EUR][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	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
2	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2462753	NMD3	trans	parietal	SCAN
rs2462753	PANX1	cis	cerebellum	SCAN
rs2462753	GPR83	cis	cerebellum	SCAN
rs2462753	PANX1	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93769800-93787800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:93778200-93784000	Weak transcription	HMEC	breast
3	chr11:93780200-93793800	Weak transcription	Fetal Intestine Large	intestine
4	chr11:93780400-93781600	Enhancers	K562	blood
5	chr11:93780400-93782000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:93780400-93782600	Weak transcription	NHEK	skin
7	chr11:93780600-93787800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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