Variant report

Variant	rs7586028
Chromosome Location	chr2:86819409-86819410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86819094..86820925-chr2:86844374..86847111,2	MCF-7	breast:
2	chr2:86788344..86791163-chr2:86817304..86820517,4	MCF-7	breast:
3	chr2:86815800..86817434-chr2:86817538..86820109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction
ENSG00000228363	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1030886	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1030887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11127043	1.00[CEU][hapmap];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	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1518812	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027265	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027270	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027280	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17027296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34605051	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];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	0.81[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	0.89[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	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59895355	1.00[EUR][1000 genomes]
rs60073472	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60244636	0.87[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]
rs60796561	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];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	0.81[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	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7579234	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7585722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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[CEU][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][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	nsv818064	chr2:86818868-86819409	Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7586028	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs7586028	MRPL35	cis	parietal	SCAN
rs7586028	VPS24	cis	parietal	SCAN
rs7586028	NDUFB6	trans	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86819000-86823400	Enhancers	Colon Smooth Muscle	Colon
2	chr2:86819200-86819800	Enhancers	Fetal Brain Female	brain
3	chr2:86819200-86820200	Enhancers	Stomach Smooth Muscle	stomach
4	chr2:86819200-86821800	Enhancers	Rectal Smooth Muscle	rectum
5	chr2:86819400-86820200	Enhancers	Fetal Brain Male	brain
6	chr2:86819400-86822600	Enhancers	Fetal Heart	heart

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