Variant report

Variant	rs2433240
Chromosome Location	chr11:59956823-59956824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1286182	0.92[EUR][1000 genomes]
rs1294440	0.92[EUR][1000 genomes]
rs1303617	0.92[EUR][1000 genomes]
rs1303618	0.92[EUR][1000 genomes]
rs1303619	0.92[EUR][1000 genomes]
rs1303620	0.92[EUR][1000 genomes]
rs1303622	0.92[EUR][1000 genomes]
rs1315507	0.92[EUR][1000 genomes]
rs1426252	0.87[ASN][1000 genomes]
rs1441585	0.89[EUR][1000 genomes]
rs2081546	0.87[ASN][1000 genomes]
rs2243987	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847662	0.89[EUR][1000 genomes]
rs474888	0.92[EUR][1000 genomes]
rs475494	0.92[EUR][1000 genomes]
rs475812	0.92[EUR][1000 genomes]
rs477352	0.92[EUR][1000 genomes]
rs485682	0.92[EUR][1000 genomes]
rs489297	0.92[EUR][1000 genomes]
rs500886	0.92[EUR][1000 genomes]
rs500888	0.92[EUR][1000 genomes]
rs512548	0.92[EUR][1000 genomes]
rs512555	0.92[EUR][1000 genomes]
rs519743	0.92[EUR][1000 genomes]
rs523806	0.92[EUR][1000 genomes]
rs524755	0.92[EUR][1000 genomes]
rs524995	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs528421	0.92[EUR][1000 genomes]
rs535413	0.92[EUR][1000 genomes]
rs541468	0.92[EUR][1000 genomes]
rs542665	0.92[EUR][1000 genomes]
rs546840	0.92[EUR][1000 genomes]
rs548515	0.92[EUR][1000 genomes]
rs549633	0.92[EUR][1000 genomes]
rs562442	0.92[EUR][1000 genomes]
rs562637	0.92[EUR][1000 genomes]
rs569108	0.92[EUR][1000 genomes]
rs571582	0.92[EUR][1000 genomes]
rs572084	0.92[EUR][1000 genomes]
rs573305	0.92[EUR][1000 genomes]
rs574060	0.92[EUR][1000 genomes]
rs574700	0.85[EUR][1000 genomes]
rs575103	0.92[EUR][1000 genomes]
rs575930	0.92[EUR][1000 genomes]
rs576295	0.92[EUR][1000 genomes]
rs576483	0.92[EUR][1000 genomes]
rs576616	0.92[EUR][1000 genomes]
rs578269	0.92[EUR][1000 genomes]
rs581818	1.00[ASN][1000 genomes]
rs582407	0.87[ASN][1000 genomes]
rs585540	0.86[ASN][1000 genomes]
rs587634	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588448	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs590351	0.97[ASN][1000 genomes]
rs590532	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs592496	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594414	0.87[ASN][1000 genomes]
rs595014	0.87[ASN][1000 genomes]
rs596788	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597982	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs598862	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600194	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs605820	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs607639	0.87[ASN][1000 genomes]
rs613548	0.84[ASN][1000 genomes]
rs613629	0.87[ASN][1000 genomes]
rs615405	0.87[ASN][1000 genomes]
rs620368	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624233	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625025	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636988	0.87[ASN][1000 genomes]
rs638872	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641051	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641829	0.87[ASN][1000 genomes]
rs642426	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646924	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649234	0.86[ASN][1000 genomes]
rs650777	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs650853	0.85[ASN][1000 genomes]
rs650926	0.87[ASN][1000 genomes]
rs653285	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654443	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661376	0.85[ASN][1000 genomes]
rs662674	0.86[ASN][1000 genomes]
rs668095	0.86[ASN][1000 genomes]
rs668134	0.86[ASN][1000 genomes]
rs670925	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672218	0.87[ASN][1000 genomes]
rs674971	0.87[ASN][1000 genomes]
rs675316	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675452	0.84[ASN][1000 genomes]
rs680699	0.97[ASN][1000 genomes]
rs682025	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs682739	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684977	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73485360	0.81[ASN][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	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv832174	chr11:59909267-60073908	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2433240	LAMP2	trans	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59950800-59961200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:59951600-59957400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr11:59954600-59957200	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr11:59954600-59961000	Weak transcription	Fetal Intestine Large	intestine
5	chr11:59956000-59957000	Enhancers	Primary B cells from cord blood	blood
6	chr11:59956000-59957200	Enhancers	Primary B cells from peripheral blood	blood
7	chr11:59956400-59960200	Weak transcription	Dnd41	blood
8	chr11:59956800-59957000	ZNF genes & repeats	Fetal Intestine Small	intestine

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