Variant report

Variant	rs60796561
Chromosome Location	chr2:86820350-86820351
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:
2	chr2:86788344..86791163-chr2:86817304..86820517,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction
ENSG00000228363	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1030886	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1030887	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11127043	0.95[EUR][1000 genomes]
rs11548929	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11890032	0.85[EUR][1000 genomes]
rs11891659	0.96[EUR][1000 genomes]
rs11899532	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1437614	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1518808	0.87[EUR][1000 genomes]
rs1518810	0.85[EUR][1000 genomes]
rs1518812	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027265	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027270	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027280	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17027296	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34605051	0.85[EUR][1000 genomes]
rs34633268	0.87[EUR][1000 genomes]
rs55688177	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55708352	0.96[EUR][1000 genomes]
rs55828608	0.87[EUR][1000 genomes]
rs56055358	0.85[EUR][1000 genomes]
rs56085540	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56169889	0.87[EUR][1000 genomes]
rs56211578	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56227180	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56242451	0.85[EUR][1000 genomes]
rs56347930	0.87[EUR][1000 genomes]
rs56378606	0.94[EUR][1000 genomes]
rs57291816	0.87[EUR][1000 genomes]
rs57836876	0.85[EUR][1000 genomes]
rs58091125	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58361202	0.87[EUR][1000 genomes]
rs58829418	0.85[EUR][1000 genomes]
rs59026369	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59183618	0.83[EUR][1000 genomes]
rs59255035	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59336972	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59521243	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59613942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59859947	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59895355	1.00[EUR][1000 genomes]
rs60073472	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60244636	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60304516	0.87[EUR][1000 genomes]
rs60717666	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60810860	0.85[EUR][1000 genomes]
rs61028062	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61465748	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61547860	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6710780	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6720414	1.00[EUR][1000 genomes]
rs6740863	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6745875	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72930315	0.87[EUR][1000 genomes]
rs72930323	0.87[EUR][1000 genomes]
rs72930336	0.87[EUR][1000 genomes]
rs72930340	0.87[EUR][1000 genomes]
rs72930349	0.87[EUR][1000 genomes]
rs72930361	0.87[EUR][1000 genomes]
rs72930362	0.87[EUR][1000 genomes]
rs72930364	0.87[EUR][1000 genomes]
rs72930369	0.87[EUR][1000 genomes]
rs72930387	0.85[EUR][1000 genomes]
rs72930396	0.83[EUR][1000 genomes]
rs72930400	0.83[EUR][1000 genomes]
rs72932307	0.85[EUR][1000 genomes]
rs72932310	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932311	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932316	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932319	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932336	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932350	0.96[EUR][1000 genomes]
rs72932358	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932364	0.96[EUR][1000 genomes]
rs72932369	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932380	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73949838	0.94[EUR][1000 genomes]
rs73949839	0.94[EUR][1000 genomes]
rs7562493	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7585722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7586028	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7604179	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7608800	1.00[AMR][1000 genomes];0.96[EUR][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
rs60796561	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 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	chr2:86819800-86820400	Enhancers	Fetal Stomach	stomach
5	chr2:86819800-86831000	Weak transcription	Fetal Brain Female	brain
6	chr2:86820000-86830600	Weak transcription	Brain Anterior Caudate	brain
7	chr2:86820000-86830800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:86820200-86831000	Weak transcription	Fetal Brain Male	brain
9	chr2:86820200-86831000	Weak transcription	Stomach Smooth Muscle	stomach

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