Variant report

Variant	rs12991654
Chromosome Location	chr2:86802854-86802855
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86789062..86793167-chr2:86801571..86804924,6	K562	blood:
2	chr2:86789199..86790708-chr2:86801917..86804757,2	K562	blood:
3	chr2:86790063..86792963-chr2:86801689..86804055,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction
ENSG00000228363	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1015117	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10169746	1.00[ASN][1000 genomes]
rs10184879	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184985	0.83[ASN][1000 genomes]
rs10187753	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10187880	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10188515	0.89[ASN][1000 genomes]
rs1020306	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10432704	0.98[ASN][1000 genomes]
rs1080551	1.00[ASN][1000 genomes]
rs11127045	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11127046	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1137684	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11676576	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11684230	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11689330	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689593	0.95[ASN][1000 genomes]
rs12328637	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12613282	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614447	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12615285	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12623509	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12714188	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714190	0.93[ASN][1000 genomes]
rs12714199	1.00[ASN][1000 genomes]
rs12987172	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015620	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034615	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13390713	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13408041	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13429696	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1518807	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1629293	0.95[ASN][1000 genomes]
rs218059	0.93[ASN][1000 genomes]
rs2367546	0.82[ASN][1000 genomes]
rs308900	0.82[ASN][1000 genomes]
rs3201448	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34666164	1.00[ASN][1000 genomes]
rs3731812	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs422240	0.81[ASN][1000 genomes]
rs4832040	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4832041	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4832042	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832043	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832045	0.97[ASN][1000 genomes]
rs4832296	0.93[ASN][1000 genomes]
rs4832297	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4832299	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4832300	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832302	1.00[ASN][1000 genomes]
rs4832303	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4832304	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62147239	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6728211	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6731025	0.87[ASN][1000 genomes]
rs6733569	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6738663	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6750226	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6752371	0.98[ASN][1000 genomes]
rs7369138	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7568840	0.83[ASN][1000 genomes]
rs7570640	1.00[ASN][1000 genomes]
rs7584882	0.98[ASN][1000 genomes]
rs7593151	0.93[ASN][1000 genomes]
rs7596717	0.93[ASN][1000 genomes]
rs7601115	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8179729	0.93[ASN][1000 genomes]
rs9284788	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12991654	VPS24	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86801400-86805800	Enhancers	Primary neutrophils fromperipheralblood	blood

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