Variant report

Variant	rs61028062
Chromosome Location	chr2:86716081-86716082
allele	A/C
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	POLR2A	chr2:86715717-86716158	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:86715562-86716303	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:86715752-86717313	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:86715716-86716237	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:86715363-86717686	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:86715632-86716270	K562	blood:	n/a	n/a
7	POLR2A	chr2:86715640-86716126	GM12892	blood:	n/a	n/a
8	POLR2A	chr2:86715720-86716267	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:86715601-86716224	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:86715991-86716281	K562	blood:	n/a	n/a
11	POLR2A	chr2:86715675-86717343	A549	lung:	n/a	n/a
12	POLR2A	chr2:86715754-86716243	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86666553..86668600-chr2:86715383..86717165,2	K562	blood:

Variant related genes	Relation type
KDM3A	TF binding region
ENSG00000115548	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	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1030887	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11127043	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11548929	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11890032	0.81[EUR][1000 genomes]
rs11891659	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11899532	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1437614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1518808	0.96[EUR][1000 genomes]
rs1518810	0.93[EUR][1000 genomes]
rs1518812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027270	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027280	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027296	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34605051	0.98[EUR][1000 genomes]
rs34633268	0.93[EUR][1000 genomes]
rs55688177	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55708352	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55828608	0.96[EUR][1000 genomes]
rs56055358	0.98[EUR][1000 genomes]
rs56085540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56169889	0.96[EUR][1000 genomes]
rs56211578	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56227180	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56242451	0.93[EUR][1000 genomes]
rs56347930	0.96[EUR][1000 genomes]
rs56378606	0.82[EUR][1000 genomes]
rs57291816	0.96[EUR][1000 genomes]
rs57836876	0.98[EUR][1000 genomes]
rs58091125	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58361202	0.96[EUR][1000 genomes]
rs58829418	0.98[EUR][1000 genomes]
rs59026369	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59183618	0.96[EUR][1000 genomes]
rs59255035	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59336972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59521243	0.87[EUR][1000 genomes]
rs59613942	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59859947	0.87[EUR][1000 genomes]
rs59895355	0.87[EUR][1000 genomes]
rs60073472	0.87[EUR][1000 genomes]
rs60244636	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60304516	0.96[EUR][1000 genomes]
rs60717666	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60796561	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60810860	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61465748	0.87[EUR][1000 genomes]
rs61547860	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6710780	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6720414	0.87[EUR][1000 genomes]
rs6740863	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6745875	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72930315	0.96[EUR][1000 genomes]
rs72930323	0.96[EUR][1000 genomes]
rs72930336	0.96[EUR][1000 genomes]
rs72930340	0.96[EUR][1000 genomes]
rs72930349	0.96[EUR][1000 genomes]
rs72930361	0.96[EUR][1000 genomes]
rs72930362	0.96[EUR][1000 genomes]
rs72930364	0.96[EUR][1000 genomes]
rs72930369	0.96[EUR][1000 genomes]
rs72930387	0.98[EUR][1000 genomes]
rs72930396	0.96[EUR][1000 genomes]
rs72930400	0.96[EUR][1000 genomes]
rs72932307	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932316	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932336	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932350	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932358	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932364	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932369	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932380	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73949838	0.82[EUR][1000 genomes]
rs73949839	0.82[EUR][1000 genomes]
rs7562493	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7585722	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7586028	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7604179	0.91[EUR][1000 genomes]
rs7608800	0.80[AMR][1000 genomes];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
rs61028062	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:86671400-86722600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:86671400-86725600	Strong transcription	A549	lung
4	chr2:86671600-86719800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr2:86671600-86723600	Strong transcription	Fetal Thymus	thymus
6	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:86672600-86721200	Strong transcription	Fetal Intestine Large	intestine
9	chr2:86672600-86724200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:86674600-86721400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:86676400-86722600	Strong transcription	GM12878-XiMat	blood
13	chr2:86676600-86721600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:86679600-86721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:86679600-86721800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:86680200-86722200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:86681000-86720800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:86681600-86722600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr2:86682000-86718600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
25	chr2:86684000-86720800	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:86684000-86726000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr2:86690200-86723200	Strong transcription	Primary B cells from cord blood	blood
28	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr2:86696800-86720600	Strong transcription	Hela-S3	cervix
30	chr2:86697000-86719200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:86697000-86719800	Strong transcription	Thymus	Thymus
32	chr2:86697000-86721200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:86697000-86721400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr2:86697200-86724600	Strong transcription	Dnd41	blood
35	chr2:86697400-86721000	Strong transcription	HUVEC	blood vessel
36	chr2:86697400-86721600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:86697600-86723000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:86697800-86721600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood
41	chr2:86698200-86720400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:86699400-86727000	Strong transcription	Placenta	Placenta
43	chr2:86699800-86717000	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:86699800-86718200	Strong transcription	Fetal Stomach	stomach
45	chr2:86699800-86718600	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr2:86699800-86719800	Strong transcription	K562	blood
47	chr2:86700400-86720800	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr2:86701000-86725600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:86702400-86721000	Strong transcription	Fetal Brain Female	brain
50	chr2:86703800-86719400	Strong transcription	Spleen	Spleen

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