Variant report

Variant	rs581949
Chromosome Location	chr12:10149406-10149407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1746123	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273986	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2760953	0.85[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2922161	0.86[EUR][1000 genomes]
rs2961542	0.88[EUR][1000 genomes]
rs2984956	0.88[EUR][1000 genomes]
rs4764178	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4764179	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4764180	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs476564	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs477658	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs477751	0.86[EUR][1000 genomes]
rs478829	0.81[CEU][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs479624	0.81[CEU][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs483576	0.86[EUR][1000 genomes]
rs525013	0.92[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs526157	0.85[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs531425	0.91[MEX][hapmap]
rs542700	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs562627	0.88[EUR][1000 genomes]
rs562839	0.88[EUR][1000 genomes]
rs566505	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582968	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs584856	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs611819	0.86[EUR][1000 genomes]
rs611821	0.86[EUR][1000 genomes]
rs612227	0.86[EUR][1000 genomes]
rs612270	0.84[EUR][1000 genomes]
rs613871	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs617956	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs640817	0.85[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs643003	0.88[EUR][1000 genomes]
rs7137254	0.86[EUR][1000 genomes]
rs7953702	0.86[EUR][1000 genomes]
rs7953814	0.85[EUR][1000 genomes]
rs7977955	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7977964	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7980924	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935538	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043125	chr12:10121288-10177037	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1042106	chr12:10121288-10177636	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1040610	chr12:10121288-10179374	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525593	chr12:10121347-10156646	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv898756	chr12:10142538-10174314	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv604	chr12:10144039-10160440	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs581949	PRB3	cis	cerebellum	SCAN
rs581949	NANOGNB	cis	parietal	SCAN
rs581949	CLEC12A	cis	normal skin	skin_eQTL
rs581949	GABARAPL1	cis	cerebellum	SCAN
rs581949	CLEC12A	cis	Nerve Tibial	GTEx
rs581949	PRH2	cis	parietal	SCAN
rs581949	RP11-133L14.5	cis	Whole Blood	GTEx
rs581949	CLEC12A	cis	Whole Blood	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10145200-10155400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr12:10145200-10155800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:10145800-10153400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:10149400-10149800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:10149400-10150000	Enhancers	Placenta Amnion	Placenta Amnion

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