Variant report

Variant	rs2367546
Chromosome Location	chr2:86820804-86820805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86819094..86820925-chr2:86844374..86847111,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10169746	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10184584	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10184879	0.82[ASN][1000 genomes]
rs10184985	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10187753	0.83[ASN][1000 genomes]
rs10432704	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1080551	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11127047	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11689330	0.82[ASN][1000 genomes]
rs11689593	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12623509	0.99[ASN][1000 genomes]
rs12714190	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12714199	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12991654	0.82[ASN][1000 genomes]
rs34666164	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832042	0.83[ASN][1000 genomes]
rs4832043	1.00[ASN][1000 genomes]
rs4832302	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832303	0.83[ASN][1000 genomes]
rs62147239	0.81[ASN][1000 genomes]
rs6733569	0.83[ASN][1000 genomes]
rs6752371	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7557796	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7568840	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7570640	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7584882	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7587034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[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
rs2367546	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86819000-86823400	Enhancers	Colon Smooth Muscle	Colon
2	chr2:86819200-86821800	Enhancers	Rectal Smooth Muscle	rectum
3	chr2:86819400-86822600	Enhancers	Fetal Heart	heart
4	chr2:86819800-86831000	Weak transcription	Fetal Brain Female	brain
5	chr2:86820000-86830600	Weak transcription	Brain Anterior Caudate	brain
6	chr2:86820000-86830800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:86820200-86831000	Weak transcription	Fetal Brain Male	brain
8	chr2:86820200-86831000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:86820400-86828400	Weak transcription	Fetal Stomach	stomach
10	chr2:86820600-86831000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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