Variant report

Variant	rs1504443
Chromosome Location	chr12:60656316-60656317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10506408	0.83[ASN][1000 genomes]
rs10747870	0.88[EUR][1000 genomes]
rs10784033	0.80[EUR][1000 genomes]
rs10877399	0.80[EUR][1000 genomes]
rs10877402	0.80[EUR][1000 genomes]
rs10877403	0.89[CEU][hapmap];0.89[GIH][hapmap];0.81[EUR][1000 genomes]
rs10877406	0.81[EUR][1000 genomes]
rs10877413	0.80[ASN][1000 genomes]
rs11173328	0.81[ASN][1000 genomes]
rs11173329	0.84[ASN][1000 genomes]
rs11173336	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11173337	0.81[ASN][1000 genomes]
rs11173339	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11173340	0.81[ASN][1000 genomes]
rs11173341	0.81[ASN][1000 genomes]
rs11173343	0.83[ASN][1000 genomes]
rs11173345	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11173346	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11173351	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11173359	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173361	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173367	0.89[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173371	0.83[EUR][1000 genomes]
rs11173386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173387	0.88[EUR][1000 genomes]
rs11173389	0.80[ASN][1000 genomes]
rs11173391	0.80[ASN][1000 genomes]
rs11173392	0.80[ASN][1000 genomes]
rs11173396	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173407	0.80[EUR][1000 genomes]
rs11173416	0.90[JPT][hapmap]
rs1125188	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12226976	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12227514	0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs12228823	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230599	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12230817	0.81[ASN][1000 genomes]
rs12231312	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12231943	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12817959	0.86[EUR][1000 genomes]
rs12830074	0.83[EUR][1000 genomes]
rs1304313	0.88[EUR][1000 genomes]
rs1319775	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1354469	0.87[EUR][1000 genomes]
rs1493318	0.81[EUR][1000 genomes]
rs1493325	0.81[ASN][1000 genomes]
rs1504442	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504444	0.83[EUR][1000 genomes]
rs1587821	0.88[EUR][1000 genomes]
rs17595010	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17595325	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17595367	0.83[ASN][1000 genomes]
rs17602381	0.85[ASN][1000 genomes]
rs17665306	0.82[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.83[ASN][1000 genomes]
rs1910674	0.89[EUR][1000 genomes]
rs2134882	0.87[EUR][1000 genomes]
rs35713358	0.85[EUR][1000 genomes]
rs3901470	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4143650	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4254103	0.81[EUR][1000 genomes]
rs4265627	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4347425	0.84[EUR][1000 genomes]
rs4366523	0.81[EUR][1000 genomes]
rs4417318	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4454757	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4491264	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4567505	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4638340	0.80[EUR][1000 genomes]
rs4758743	0.81[ASN][1000 genomes]
rs4758744	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4758745	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4758859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55661627	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61487567	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61923065	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61923066	0.83[ASN][1000 genomes]
rs61923067	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61923074	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61923092	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61923093	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61923121	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61923127	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61923129	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61923130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61923132	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61923155	0.80[ASN][1000 genomes]
rs61923156	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61923157	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61925366	0.81[ASN][1000 genomes]
rs61925560	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581305	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66587505	0.81[ASN][1000 genomes]
rs7131926	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7134267	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136435	0.86[EUR][1000 genomes]
rs7136835	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138626	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72648145	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7297548	0.86[EUR][1000 genomes]
rs7305978	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7312225	0.83[EUR][1000 genomes]
rs7313364	0.86[EUR][1000 genomes]
rs7953857	0.80[ASN][1000 genomes]
rs7957100	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961221	0.86[EUR][1000 genomes]
rs7973882	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8181648	0.81[CHB][hapmap]
rs905722	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs924835	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs958543	0.89[EUR][1000 genomes]
rs959645	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9634280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634281	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668893	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[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	nsv899137	chr12:60568891-60797083	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1054287	chr12:60601870-60861866	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv832431	chr12:60626292-60809233	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1504443	RDH5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60651400-60656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:60656200-60656800	Enhancers	A549	lung
3	chr12:60656200-60657200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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