Variant report

Variant	rs61465748
Chromosome Location	chr2:86789525-86789526
allele	G/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	MYC	chr2:86789472-86789538	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr2:86789489-86789679	MCF10A-Er-Src	breast:	n/a	n/a
3	MYBL2	chr2:86789421-86791040	HepG2	liver:	n/a	n/a
4	RELA	chr2:86789420-86790881	GM19099	blood:	n/a	n/a
5	POLR2A	chr2:86789199-86791048	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:86789310-86791036	HUVEC	blood vessel:	n/a	n/a
7	SMARCC1	chr2:86789466-86791076	Hela-S3	cervix:	n/a	n/a
8	MBD4	chr2:86789523-86790976	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:86789513-86791000	GM12878	blood:	n/a	n/a
10	CTCF	chr2:86789500-86789650	NB4	blood:	n/a	n/a
11	MAZ	chr2:86789393-86791145	IMR90	lung:	n/a	n/a
12	POLR2A	chr2:86789462-86791005	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr2:86789497-86790786	HepG2	liver:	n/a	n/a
14	FOS	chr2:86789493-86789574	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr2:86789051-86790836	GM12878	blood:	n/a	n/a
16	TCF12	chr2:86789467-86791205	A549	lung:	n/a	n/a
17	JUND	chr2:86789315-86791538	SK-N-SH	brain:	n/a	chr2:86790669-86790678
18	USF2	chr2:86789515-86789959	Hela-S3	cervix:	n/a	n/a
19	REST	chr2:86789429-86791172	H1-neurons	neurons:	n/a	n/a
20	SREBP1	chr2:86789371-86791526	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:86788139-86791058	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr2:86789473-86790957	GM12891	blood:	n/a	n/a
23	CHD1	chr2:86789255-86791674	IMR90	lung:	n/a	n/a
24	POLR2A	chr2:86789464-86791117	Hela-S3	cervix:	n/a	n/a
25	FOS	chr2:86789510-86789585	MCF10A-Er-Src	breast:	n/a	n/a
26	PML	chr2:86789506-86791060	GM12878	blood:	n/a	n/a
27	JUN	chr2:86789416-86791921	K562	blood:	n/a	chr2:86790669-86790678 chr2:86790665-86790678
28	POLR2A	chr2:86789450-86790924	PANC-1	pancreas:	n/a	n/a
29	RELA	chr2:86789423-86790916	GM15510	blood:	n/a	n/a
30	WRNIP1	chr2:86789412-86789673	GM12878	blood:	n/a	n/a
31	GABPA	chr2:86789525-86790789	A549	lung:	n/a	chr2:86790625-86790639 chr2:86790007-86790016 chr2:86790609-86790623 chr2:86790627-86790636 chr2:86790614-86790623 chr2:86790612-86790623 chr2:86790625-86790636 chr2:86790612-86790621 chr2:86790612-86790626
32	POLR2A	chr2:86789430-86790821	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:86788930-86791074	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr2:86789356-86791107	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86789208..86791396-chr2:86847374..86850220,3	K562	blood:
2	chr2:86788265..86792368-chr2:86847223..86851122,9	MCF-7	breast:
3	chr2:86787885..86791617-chr2:86846945..86852237,10	MCF-7	breast:
4	chr2:86667181..86671352-chr2:86788569..86792016,9	K562	blood:
5	chr2:86675470..86677064-chr2:86789067..86791804,2	K562	blood:
6	chr2:86683337..86686158-chr2:86788468..86790099,2	K562	blood:
7	chr2:86788830..86791431-chr2:86840608..86843450,2	MCF-7	breast:
8	chr2:86667867..86670714-chr2:86788591..86792016,6	K562	blood:
9	chr2:86768330..86770893-chr2:86788631..86790351,2	MCF-7	breast:
10	chr2:86768416..86770148-chr2:86788776..86791122,2	K562	blood:
11	chr2:86789208..86791396-chr2:86848677..86850220,2	K562	blood:
12	chr2:86789024..86791664-chr2:87302659..87304185,2	MCF-7	breast:

Variant related genes	Relation type
CHMP3	TF binding region
ENSG00000115548	Chromatin interaction
ENSG00000115561	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000231259	Chromatin interaction
ENSG00000249884	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	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1030887	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11127043	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11548929	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11890032	0.85[EUR][1000 genomes]
rs11891659	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11899532	0.87[EUR][1000 genomes]
rs1437614	0.89[EUR][1000 genomes]
rs1518808	0.87[EUR][1000 genomes]
rs1518810	0.85[EUR][1000 genomes]
rs1518812	0.87[EUR][1000 genomes]
rs17027265	0.87[EUR][1000 genomes]
rs17027270	0.87[EUR][1000 genomes]
rs17027280	0.96[EUR][1000 genomes]
rs17027296	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34605051	0.85[EUR][1000 genomes]
rs34633268	0.87[EUR][1000 genomes]
rs55688177	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55708352	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55828608	0.87[EUR][1000 genomes]
rs56055358	0.85[EUR][1000 genomes]
rs56085540	0.87[EUR][1000 genomes]
rs56169889	0.87[EUR][1000 genomes]
rs56211578	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56227180	0.97[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	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58361202	0.87[EUR][1000 genomes]
rs58829418	0.85[EUR][1000 genomes]
rs59026369	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59183618	0.83[EUR][1000 genomes]
rs59255035	0.85[EUR][1000 genomes]
rs59336972	0.87[EUR][1000 genomes]
rs59521243	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59613942	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59859947	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59895355	1.00[EUR][1000 genomes]
rs60073472	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60244636	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60304516	0.87[EUR][1000 genomes]
rs60717666	0.85[EUR][1000 genomes]
rs60796561	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60810860	0.85[EUR][1000 genomes]
rs61028062	0.87[EUR][1000 genomes]
rs61547860	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6710780	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6720414	1.00[EUR][1000 genomes]
rs6740863	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6745875	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	0.87[EUR][1000 genomes]
rs72932311	0.87[EUR][1000 genomes]
rs72932316	0.87[EUR][1000 genomes]
rs72932319	0.87[EUR][1000 genomes]
rs72932336	0.96[EUR][1000 genomes]
rs72932350	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932358	0.96[EUR][1000 genomes]
rs72932364	0.96[EUR][1000 genomes]
rs72932369	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932380	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73949838	0.94[EUR][1000 genomes]
rs73949839	0.94[EUR][1000 genomes]
rs7562493	0.96[EUR][1000 genomes]
rs7585722	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7586028	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7604179	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7608800	0.97[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
rs61465748	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86777400-86789600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:86780800-86789600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:86786400-86789600	Weak transcription	Gastric	stomach
4	chr2:86788600-86789600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr2:86788600-86789600	Weak transcription	Ovary	ovary
6	chr2:86788600-86789800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr2:86788600-86790000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr2:86788600-86790200	Active TSS	Right Atrium	heart
9	chr2:86788800-86789600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:86788800-86789600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:86788800-86789600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:86788800-86789600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr2:86788800-86789600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr2:86788800-86789600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr2:86788800-86789600	Flanking Active TSS	A549	lung
16	chr2:86788800-86789800	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr2:86788800-86790600	Active TSS	Fetal Kidney	kidney
18	chr2:86789000-86789600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr2:86789000-86789600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr2:86789000-86789600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr2:86789000-86789600	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr2:86789000-86789600	Flanking Active TSS	Fetal Lung	lung
23	chr2:86789000-86789600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr2:86789000-86789600	Flanking Active TSS	HepG2	liver
25	chr2:86789000-86789600	Flanking Active TSS	HMEC	breast
26	chr2:86789000-86789600	Flanking Active TSS	NHEK	skin
27	chr2:86789000-86789800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:86789000-86789800	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr2:86789000-86789800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:86789000-86789800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:86789000-86789800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:86789000-86789800	Flanking Active TSS	Liver	Liver
33	chr2:86789000-86789800	Flanking Active TSS	Dnd41	blood
34	chr2:86789000-86789800	Flanking Active TSS	HUVEC	blood vessel
35	chr2:86789000-86789800	Flanking Active TSS	Osteobl	bone
36	chr2:86789000-86790000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr2:86789000-86790000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:86789000-86790600	Active TSS	Right Ventricle	heart
39	chr2:86789000-86790800	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr2:86789200-86789600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr2:86789200-86789600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr2:86789200-86789600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr2:86789200-86789600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr2:86789200-86789600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:86789200-86789600	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr2:86789200-86789600	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr2:86789200-86789600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr2:86789200-86789600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:86789200-86789600	Flanking Active TSS	Fetal Brain Male	brain
50	chr2:86789200-86789600	Flanking Active TSS	Fetal Brain Female	brain

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