Variant report

Variant	rs4113946
Chromosome Location	chr12:49024020-49024021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10747554	0.83[ASN][1000 genomes]
rs10783273	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783274	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10783275	0.85[ASN][1000 genomes]
rs10783278	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875849	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10875850	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875852	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875853	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875861	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10875862	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875863	0.81[EUR][1000 genomes]
rs1110432	0.82[ASN][1000 genomes]
rs11168657	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168665	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168674	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168681	0.81[CEU][hapmap];0.93[TSI][hapmap]
rs11168697	0.86[EUR][1000 genomes]
rs11168698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168702	0.81[JPT][hapmap]
rs12299955	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12426435	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1316514	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1863541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1895995	0.94[ASN][1000 genomes]
rs2114320	0.83[ASN][1000 genomes]
rs2162317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2277365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2291728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2409085	0.93[ASN][1000 genomes]
rs2898087	0.94[ASN][1000 genomes]
rs3209584	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs35717253	0.94[ASN][1000 genomes]
rs3741628	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3741629	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3741630	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3741632	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3803025	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3943899	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4500528	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760735	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760737	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760739	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760740	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6580689	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6580690	0.94[ASN][1000 genomes]
rs7133756	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7136021	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7138190	0.94[ASN][1000 genomes]
rs7139236	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7299276	0.92[ASN][1000 genomes]
rs7304711	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305907	0.82[ASN][1000 genomes]
rs7306604	0.86[ASN][1000 genomes]
rs7308699	0.88[ASN][1000 genomes]
rs7308932	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7314665	0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7954446	0.81[ASN][1000 genomes]
rs7954548	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs7964546	0.85[ASN][1000 genomes]
rs7966065	0.99[ASN][1000 genomes]
rs7973824	0.86[ASN][1000 genomes]
rs7974151	0.80[ASN][1000 genomes]
rs7974625	0.82[ASN][1000 genomes]
rs7975030	0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7975821	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332441	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9634241	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9634242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9634262	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4113946	C12orf41	cis	cerebellum	SCAN
rs4113946	FLJ20436	cis	multi-tissue	Pritchard
rs4113946	FAM186B	cis	cerebellum	SCAN
rs4113946	KANSL2	cis	lung	GTEx
rs4113946	C12orf41	cis	parietal	SCAN
rs4113946	KANSL2	cis	Thyroid	GTEx
rs4113946	KANSL2	cis	Esophagus Mucosa	GTEx
rs4113946	KANSL2	cis	Nerve Tibial	GTEx
rs4113946	KANSL2	cis	Artery Tibial	GTEx
rs4113946	KANSL2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49023200-49024200	Enhancers	GM12878-XiMat	blood
2	chr12:49023800-49024600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:49024000-49025200	Weak transcription	Placenta Amnion	Placenta Amnion

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