Variant report

Variant	rs56378606
Chromosome Location	chr2:86826271-86826272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr2:86826025-86826381	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr2:86826054-86826396	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr2:86825990-86826499	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr2:86826099-86826466	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr2:86826022-86826385	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr2:86825949-86826992	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr2:86826014-86826578	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr2:86826035-86826395	MCF10A-Er-Src	breast:	n/a	n/a
9	E2F4	chr2:86826157-86826394	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr2:86826020-86826473	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr2:86826256-86826339	K562	blood:	n/a	n/a
12	STAT3	chr2:86826024-86826408	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr2:86826036-86826395	MCF10A-Er-Src	breast:	n/a	n/a
14	TCF7L2	chr2:86826041-86826410	HepG2	liver:	n/a	n/a
15	FOS	chr2:86825992-86826482	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86825844..86830459-chr2:86849493..86852270,4	MCF-7	breast:
2	chr2:86825748..86827499-chr2:86830079..86832561,2	K562	blood:

Variant related genes	Relation type
ENSG00000228363	TF binding region
ENSG00000249884	Chromatin interaction
ENSG00000228363	Chromatin interaction
ENSG00000239305	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1030886	0.90[EUR][1000 genomes]
rs1030887	0.90[EUR][1000 genomes]
rs11127043	0.89[EUR][1000 genomes]
rs11548929	0.90[EUR][1000 genomes]
rs11891659	0.90[EUR][1000 genomes]
rs11899532	0.82[EUR][1000 genomes]
rs1437614	0.84[EUR][1000 genomes]
rs1518808	0.82[EUR][1000 genomes]
rs1518812	0.82[EUR][1000 genomes]
rs17027265	0.82[EUR][1000 genomes]
rs17027270	0.82[EUR][1000 genomes]
rs17027280	0.90[EUR][1000 genomes]
rs17027296	0.94[EUR][1000 genomes]
rs34633268	0.81[EUR][1000 genomes]
rs55688177	0.90[EUR][1000 genomes]
rs55708352	0.90[EUR][1000 genomes]
rs55828608	0.82[EUR][1000 genomes]
rs56085540	0.82[EUR][1000 genomes]
rs56169889	0.82[EUR][1000 genomes]
rs56211578	0.92[EUR][1000 genomes]
rs56227180	0.94[EUR][1000 genomes]
rs56347930	0.82[EUR][1000 genomes]
rs57291816	0.82[EUR][1000 genomes]
rs58091125	0.94[EUR][1000 genomes]
rs58361202	0.82[EUR][1000 genomes]
rs59026369	0.94[EUR][1000 genomes]
rs59336972	0.82[EUR][1000 genomes]
rs59521243	0.94[EUR][1000 genomes]
rs59613942	0.94[EUR][1000 genomes]
rs59859947	0.94[EUR][1000 genomes]
rs59895355	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60073472	0.94[EUR][1000 genomes]
rs60244636	0.94[EUR][1000 genomes]
rs60304516	0.82[EUR][1000 genomes]
rs60796561	0.94[EUR][1000 genomes]
rs61028062	0.82[EUR][1000 genomes]
rs61465748	0.94[EUR][1000 genomes]
rs61547860	0.90[EUR][1000 genomes]
rs6710780	0.90[EUR][1000 genomes]
rs6720414	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6740863	0.90[EUR][1000 genomes]
rs6745875	0.90[EUR][1000 genomes]
rs72930315	0.82[EUR][1000 genomes]
rs72930323	0.82[EUR][1000 genomes]
rs72930336	0.82[EUR][1000 genomes]
rs72930340	0.82[EUR][1000 genomes]
rs72930349	0.82[EUR][1000 genomes]
rs72930361	0.82[EUR][1000 genomes]
rs72930362	0.82[EUR][1000 genomes]
rs72930364	0.82[EUR][1000 genomes]
rs72930369	0.82[EUR][1000 genomes]
rs72932310	0.82[EUR][1000 genomes]
rs72932311	0.82[EUR][1000 genomes]
rs72932316	0.82[EUR][1000 genomes]
rs72932319	0.82[EUR][1000 genomes]
rs72932336	0.90[EUR][1000 genomes]
rs72932350	0.90[EUR][1000 genomes]
rs72932358	0.90[EUR][1000 genomes]
rs72932364	0.90[EUR][1000 genomes]
rs72932369	0.90[EUR][1000 genomes]
rs72932380	0.94[EUR][1000 genomes]
rs73949838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73949839	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7562493	0.90[EUR][1000 genomes]
rs7585722	0.94[EUR][1000 genomes]
rs7586028	0.94[EUR][1000 genomes]
rs7604179	0.90[EUR][1000 genomes]
rs7608800	0.90[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	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
rs56378606	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 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	chr2:86823600-86831200	Weak transcription	HSMMtube	muscle
11	chr2:86824000-86830800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:86824000-86831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:86824600-86840600	Weak transcription	Fetal Heart	heart
14	chr2:86824800-86831000	Weak transcription	Left Ventricle	heart
15	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:86825600-86830600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:86825800-86826600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:86825800-86826800	Enhancers	NHEK	skin
19	chr2:86825800-86831000	Weak transcription	Liver	Liver
20	chr2:86826000-86826600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:86826000-86826600	Enhancers	HMEC	breast
22	chr2:86826000-86826800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:86826000-86831000	Weak transcription	HUVEC	blood vessel
24	chr2:86826200-86826400	Enhancers	Stomach Mucosa	stomach
25	chr2:86826200-86826400	Enhancers	Hela-S3	cervix
26	chr2:86826200-86826600	Enhancers	Colon Smooth Muscle	Colon
27	chr2:86826200-86826800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:86826200-86826800	Enhancers	Rectal Smooth Muscle	rectum

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