Variant report

Variant	rs539567
Chromosome Location	chr11:58472765-58472766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10792184	0.82[JPT][hapmap]
rs10792185	0.82[JPT][hapmap]
rs10896818	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10896820	0.82[EUR][1000 genomes]
rs10896822	0.81[EUR][1000 genomes]
rs10896825	0.82[CHB][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap]
rs10896854	0.80[JPT][hapmap]
rs10896856	0.82[JPT][hapmap]
rs10896857	0.81[JPT][hapmap]
rs10896858	0.82[JPT][hapmap]
rs10896859	0.82[JPT][hapmap]
rs11229578	0.83[AMR][1000 genomes]
rs11229593	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11229594	0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11229595	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11229596	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11229597	0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11229601	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229602	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11229603	0.83[EUR][1000 genomes]
rs11229651	0.84[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap]
rs11229655	0.84[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs11229656	0.82[JPT][hapmap]
rs11229658	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs11530801	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12225778	0.81[JPT][hapmap]
rs17152916	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17153009	0.82[JPT][hapmap]
rs1938695	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1938696	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1938698	0.82[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1938701	0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1938714	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1938728	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1938730	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1941965	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1943270	0.80[ASN][1000 genomes]
rs1943271	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1943280	0.84[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs1943281	0.82[JPT][hapmap]
rs1943282	0.82[JPT][hapmap]
rs2156346	0.82[JPT][hapmap]
rs2186414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2497372	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2497376	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2497377	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2497379	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35649133	0.83[EUR][1000 genomes]
rs3920943	0.81[EUR][1000 genomes]
rs472569	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs473287	0.82[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs479854	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs483101	0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs487054	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs491849	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs492795	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4939226	0.82[JPT][hapmap]
rs4939229	0.82[GIH][hapmap];0.94[MEX][hapmap]
rs4939230	0.82[JPT][hapmap]
rs4939231	0.82[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs507224	0.82[ASW][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs511772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521200	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs522568	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs524234	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs524516	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs528136	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs542537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs543032	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs547178	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs547654	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs547895	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs550362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558274	0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56073415	0.81[EUR][1000 genomes]
rs566084	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs570146	0.82[ASW][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs570244	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57121352	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs572006	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs572856	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs590157	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs591121	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs591628	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs596847	0.82[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs614561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621137	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs621780	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs628124	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs631103	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs667445	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs675423	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675757	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs677988	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72925740	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72925778	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72927728	0.83[EUR][1000 genomes]
rs7951340	0.80[AMR][1000 genomes];0.83[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	nsv832168	chr11:58394060-58564651	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv329	chr11:58451044-58478290	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs539567	TMX2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58469200-58474600	ZNF genes & repeats	Liver	Liver
2	chr11:58470600-58474400	ZNF genes & repeats	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links