Variant report

Variant	rs12654787
Chromosome Location	chr5:90713259-90713260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90675686..90682744-chr5:90708419..90715795,15	K562	blood:
2	chr5:90678158..90681149-chr5:90713018..90715542,3	MCF-7	breast:
3	chr5:90676294..90680859-chr5:90711811..90718660,12	K562	blood:
4	chr5:90676107..90677839-chr5:90711969..90714556,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10041402	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10045280	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10052492	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10054820	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10058025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10059163	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10063683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10073657	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10073935	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1035476	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1035477	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10474352	0.91[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10474353	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10942634	0.93[EUR][1000 genomes]
rs11948056	0.90[EUR][1000 genomes]
rs11948075	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11950530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11955120	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11959525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12110065	1.00[CEU][hapmap];0.96[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12110303	0.90[EUR][1000 genomes]
rs12188467	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12651840	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12655973	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12656350	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1363839	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs1477348	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs186717	0.86[EUR][1000 genomes]
rs1895448	0.94[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1895449	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1964292	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1966494	0.94[EUR][1000 genomes]
rs2004483	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052553	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2059207	0.94[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2059208	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2367353	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2367526	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839728	0.94[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2887007	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs332529	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs332531	0.80[EUR][1000 genomes]
rs332544	0.86[EUR][1000 genomes]
rs35712350	0.97[EUR][1000 genomes]
rs4382199	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60513756	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6452951	0.93[EUR][1000 genomes]
rs6452953	0.94[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6452954	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66759971	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6860948	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6865495	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6866191	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6866923	0.94[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes]
rs6867091	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6869048	0.93[EUR][1000 genomes]
rs6869717	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6882269	0.95[EUR][1000 genomes]
rs746637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705465	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7708782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7715402	0.94[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs7718871	0.94[CEU][hapmap];0.96[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs7720132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7720235	0.84[EUR][1000 genomes]
rs889213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9293568	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9686361	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs985434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1030453	chr5:90709080-90849693	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90712800-90713600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:90713000-90713400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:90713000-90713400	Enhancers	Osteobl	bone
4	chr5:90713000-90713600	Enhancers	Adipose Nuclei	Adipose
5	chr5:90713000-90713600	Enhancers	A549	lung
6	chr5:90713000-90715400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:90713200-90713600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:90713200-90713800	Enhancers	Colon Smooth Muscle	Colon

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