Variant report

Variant	rs34633268
Chromosome Location	chr2:86666301-86666302
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86652314..86654591-chr2:86664666..86667245,2	MCF-7	breast:
2	chr2:86664840..86667143-chr2:86695504..86697285,2	MCF-7	breast:
3	chr2:86658372..86661098-chr2:86664087..86666512,2	MCF-7	breast:
4	chr2:86665985..86667815-chr2:86739595..86741738,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHMP3-2	chr2:86664163-86667836	NONHSAT072102

Variant related genes	Relation type
ENSG00000115561	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	0.91[EUR][1000 genomes]
rs1030887	0.91[EUR][1000 genomes]
rs11127043	0.90[EUR][1000 genomes]
rs11548929	0.91[EUR][1000 genomes]
rs11890032	0.81[EUR][1000 genomes]
rs11891659	0.91[EUR][1000 genomes]
rs11899532	0.93[EUR][1000 genomes]
rs1437614	0.93[EUR][1000 genomes]
rs1518808	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1518810	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1518812	0.93[EUR][1000 genomes]
rs17027265	0.93[EUR][1000 genomes]
rs17027270	0.93[EUR][1000 genomes]
rs17027280	0.91[EUR][1000 genomes]
rs17027296	0.87[EUR][1000 genomes]
rs34605051	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55688177	0.91[EUR][1000 genomes]
rs55708352	0.91[EUR][1000 genomes]
rs55828608	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56055358	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56085540	0.93[EUR][1000 genomes]
rs56169889	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56211578	0.85[EUR][1000 genomes]
rs56227180	0.87[EUR][1000 genomes]
rs56242451	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56347930	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56378606	0.81[EUR][1000 genomes]
rs57291816	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57836876	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58091125	0.87[EUR][1000 genomes]
rs58361202	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58829418	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59026369	0.87[EUR][1000 genomes]
rs59183618	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59255035	0.96[EUR][1000 genomes]
rs59336972	0.93[EUR][1000 genomes]
rs59521243	0.87[EUR][1000 genomes]
rs59613942	0.87[EUR][1000 genomes]
rs59859947	0.87[EUR][1000 genomes]
rs59895355	0.87[EUR][1000 genomes]
rs60073472	0.87[EUR][1000 genomes]
rs60244636	0.87[EUR][1000 genomes]
rs60304516	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60717666	0.96[EUR][1000 genomes]
rs60796561	0.87[EUR][1000 genomes]
rs60810860	0.91[EUR][1000 genomes]
rs61028062	0.93[EUR][1000 genomes]
rs61465748	0.87[EUR][1000 genomes]
rs61547860	0.91[EUR][1000 genomes]
rs6710780	0.91[EUR][1000 genomes]
rs6720414	0.87[EUR][1000 genomes]
rs6740863	0.91[EUR][1000 genomes]
rs6745875	0.91[EUR][1000 genomes]
rs72930315	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930323	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930336	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930340	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930349	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930361	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930362	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930364	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930369	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930387	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72930396	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72930400	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72932307	0.96[EUR][1000 genomes]
rs72932310	0.93[EUR][1000 genomes]
rs72932311	0.93[EUR][1000 genomes]
rs72932316	0.93[EUR][1000 genomes]
rs72932319	0.93[EUR][1000 genomes]
rs72932336	0.91[EUR][1000 genomes]
rs72932350	0.91[EUR][1000 genomes]
rs72932358	0.91[EUR][1000 genomes]
rs72932364	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932369	0.91[EUR][1000 genomes]
rs72932380	0.87[EUR][1000 genomes]
rs73949838	0.81[EUR][1000 genomes]
rs73949839	0.81[EUR][1000 genomes]
rs7562493	0.91[EUR][1000 genomes]
rs7585722	0.87[EUR][1000 genomes]
rs7586028	0.87[EUR][1000 genomes]
rs7604179	0.91[EUR][1000 genomes]
rs7608800	0.91[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
rs34633268	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86665400-86667800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:86665400-86667800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
3	chr2:86665800-86666800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:86665800-86667600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:86665800-86667800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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