Variant report

Variant	rs6581305
Chromosome Location	chr12:60625938-60625939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10506408	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10747870	0.83[EUR][1000 genomes]
rs10784033	0.85[EUR][1000 genomes]
rs10877398	0.81[EUR][1000 genomes]
rs10877399	0.86[EUR][1000 genomes]
rs10877401	0.84[EUR][1000 genomes]
rs10877402	0.85[EUR][1000 genomes]
rs10877403	0.89[CEU][hapmap];0.86[GIH][hapmap];0.86[EUR][1000 genomes]
rs10877406	0.86[EUR][1000 genomes]
rs11173327	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11173328	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173329	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11173336	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173337	0.83[ASN][1000 genomes]
rs11173339	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173340	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173341	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173343	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11173345	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11173346	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11173351	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11173357	0.83[EUR][1000 genomes]
rs11173359	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11173361	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11173365	0.84[EUR][1000 genomes]
rs11173367	0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11173371	0.88[EUR][1000 genomes]
rs11173386	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11173387	0.82[EUR][1000 genomes]
rs11173396	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1125188	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12226976	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12227514	0.82[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs12228823	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12230599	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12230817	0.84[ASN][1000 genomes]
rs12231312	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12231943	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12817959	0.86[EUR][1000 genomes]
rs12830074	0.88[EUR][1000 genomes]
rs1304313	0.82[EUR][1000 genomes]
rs1319775	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354469	0.81[EUR][1000 genomes]
rs1389256	0.84[EUR][1000 genomes]
rs1493311	0.83[EUR][1000 genomes]
rs1493318	0.86[EUR][1000 genomes]
rs1493325	0.84[ASN][1000 genomes]
rs1504442	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1504443	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1504444	0.84[EUR][1000 genomes]
rs1587821	0.82[EUR][1000 genomes]
rs17595010	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17595325	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17595367	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17602381	0.87[ASN][1000 genomes]
rs17665306	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1910674	0.84[EUR][1000 genomes]
rs2134882	0.81[EUR][1000 genomes]
rs35713358	0.83[EUR][1000 genomes]
rs3901470	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4143650	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4254103	0.86[EUR][1000 genomes]
rs4265627	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4347425	0.89[EUR][1000 genomes]
rs4366523	0.86[EUR][1000 genomes]
rs4406858	0.85[EUR][1000 genomes]
rs4417318	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4454757	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4491264	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4567505	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4758743	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4758744	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4758745	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758858	0.85[EUR][1000 genomes]
rs4758859	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55661627	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61487567	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923065	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61923066	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61923067	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61923074	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923092	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61923093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61923121	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61923124	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923127	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923129	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923130	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923132	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923156	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61923157	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61925366	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61925560	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66587505	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7131926	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7134267	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7136435	0.86[EUR][1000 genomes]
rs7136835	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7138626	0.88[EUR][1000 genomes]
rs7138854	0.82[EUR][1000 genomes]
rs72648145	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305978	0.84[AMR][1000 genomes]
rs7310323	0.80[ASN][1000 genomes]
rs7314355	0.80[ASN][1000 genomes]
rs7957100	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7961221	0.86[EUR][1000 genomes]
rs7973882	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7979069	0.80[ASN][1000 genomes]
rs8181648	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs905722	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs924835	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs958543	0.83[EUR][1000 genomes]
rs959645	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9634280	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634281	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9668893	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428591	chr12:60446360-60631044	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv2754064	chr12:60608389-60645117	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6581305	RDH5	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60599600-60645400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:60625000-60627200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:60625200-60626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:60625200-60632600	Weak transcription	K562	blood

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