Variant report

Variant	rs10187753
Chromosome Location	chr2:86824922-86824923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10184584	0.99[ASN][1000 genomes]
rs10184879	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10184985	0.83[ASN][1000 genomes]
rs10187880	0.82[EUR][1000 genomes]
rs11127047	0.99[ASN][1000 genomes]
rs11689330	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12328637	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12613282	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12623509	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12987172	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12991654	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13015620	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2367546	0.83[ASN][1000 genomes]
rs308900	0.81[ASN][1000 genomes]
rs4240204	0.81[EUR][1000 genomes]
rs4832042	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4832300	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4832303	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832304	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62147239	0.81[EUR][1000 genomes]
rs6728211	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6733569	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738663	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6750226	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7568840	0.83[ASN][1000 genomes]
rs7587034	1.00[ASN][1000 genomes]
rs7601115	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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	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
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10187753	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86819800-86831000	Weak transcription	Fetal Brain Female	brain
2	chr2:86820000-86830600	Weak transcription	Brain Anterior Caudate	brain
3	chr2:86820000-86830800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:86820200-86831000	Weak transcription	Fetal Brain Male	brain
5	chr2:86820200-86831000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:86820400-86828400	Weak transcription	Fetal Stomach	stomach
7	chr2:86820600-86831000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:86823000-86830600	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:86823200-86842800	Weak transcription	Psoas Muscle	Psoas
10	chr2:86823400-86826200	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:86823600-86831200	Weak transcription	HSMMtube	muscle
12	chr2:86824000-86830800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:86824000-86831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:86824200-86826200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:86824600-86840600	Weak transcription	Fetal Heart	heart
16	chr2:86824800-86831000	Weak transcription	Left Ventricle	heart

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