Variant report

Variant	rs2468842
Chromosome Location	chr11:18154120-18154121
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18152566..18154757-chr11:18415660..18417661,2	K562	blood:

Variant related genes	Relation type
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10500831	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs10832882	0.88[ASN][1000 genomes]
rs11024460	0.81[CEU][hapmap]
rs11024468	0.88[ASN][1000 genomes]
rs11024474	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11024476	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11024478	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11024482	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs11024484	0.88[ASN][1000 genomes]
rs11024485	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs11024493	0.86[ASN][1000 genomes]
rs11024496	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12360537	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12363226	0.88[ASN][1000 genomes]
rs12364327	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs12792460	0.81[ASN][1000 genomes]
rs1399025	0.89[CHB][hapmap]
rs1824017	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1840595	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1975777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2168361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2263407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2445162	0.82[ASN][1000 genomes]
rs2468832	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2468841	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35447333	0.81[ASN][1000 genomes]
rs3741199	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4052539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4274188	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4756930	0.89[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs5790015	0.88[ASN][1000 genomes]
rs61882530	0.88[ASN][1000 genomes]
rs6486406	0.80[CHD][hapmap]
rs7119063	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs7131255	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs7131454	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7933259	0.85[ASN][1000 genomes]
rs7934091	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7942794	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs7943725	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs871699	0.89[CHB][hapmap]
rs907922	0.89[CHB][hapmap]
rs907923	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs964834	0.89[CHB][hapmap];0.81[JPT][hapmap]

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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	esv11709	chr11:18138662-18200717	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv971990	chr11:18153921-18164912	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2468842	SAAL1	cis	lung	GTEx
rs2468842	SAAL1	cis	Skin Sun Exposed Lower leg	GTEx
rs2468842	SAAL1	cis	multi-tissue	Pritchard
rs2468842	SAAL1	cis	brain	seeQTL
rs2468842	MRGPRX3	cis	Esophagus Mucosa	GTEx
rs2468842	SAAL1	cis	Artery Tibial	GTEx
rs2468842	MRGPRX3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18150400-18156200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:18151800-18154200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:18152400-18154600	Enhancers	HepG2	liver
4	chr11:18153800-18154600	Enhancers	NHEK	skin
5	chr11:18153800-18155000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:18153800-18155600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:18154000-18154200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr11:18154000-18154600	Flanking Active TSS	HMEC	breast

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