Variant report

Variant	rs60717666
Chromosome Location	chr2:86706834-86706835
allele	A/G
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	chr2:86706815-86706989	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86704223..86708236-chr2:86709425..86713459,5	K562	blood:
2	chr2:86703571..86706359-chr2:86706716..86708638,2	MCF-7	breast:
3	chr2:86667473..86669987-chr2:86705079..86707009,2	K562	blood:

Variant related genes	Relation type
KDM3A	TF binding region
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1030886	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1030887	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11127043	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11548929	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11891659	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11899532	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1437614	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1518808	0.98[EUR][1000 genomes]
rs1518810	0.96[EUR][1000 genomes]
rs1518812	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17027265	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17027270	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17027280	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17027296	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34605051	1.00[EUR][1000 genomes]
rs34633268	0.96[EUR][1000 genomes]
rs55688177	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55708352	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55828608	0.98[EUR][1000 genomes]
rs56055358	1.00[EUR][1000 genomes]
rs56085540	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56169889	0.98[EUR][1000 genomes]
rs56211578	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56227180	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56242451	0.96[EUR][1000 genomes]
rs56347930	0.98[EUR][1000 genomes]
rs57291816	0.98[EUR][1000 genomes]
rs57836876	1.00[EUR][1000 genomes]
rs58091125	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58361202	0.98[EUR][1000 genomes]
rs58829418	1.00[EUR][1000 genomes]
rs59026369	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59183618	0.98[EUR][1000 genomes]
rs59255035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59336972	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59521243	0.85[EUR][1000 genomes]
rs59613942	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59859947	0.85[EUR][1000 genomes]
rs59895355	0.85[EUR][1000 genomes]
rs60073472	0.85[EUR][1000 genomes]
rs60244636	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60304516	0.98[EUR][1000 genomes]
rs60796561	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60810860	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61028062	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61465748	0.85[EUR][1000 genomes]
rs61547860	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6710780	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6720414	0.85[EUR][1000 genomes]
rs6740863	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6745875	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72930315	0.98[EUR][1000 genomes]
rs72930323	0.98[EUR][1000 genomes]
rs72930336	0.98[EUR][1000 genomes]
rs72930340	0.98[EUR][1000 genomes]
rs72930349	0.98[EUR][1000 genomes]
rs72930361	0.98[EUR][1000 genomes]
rs72930362	0.98[EUR][1000 genomes]
rs72930364	0.98[EUR][1000 genomes]
rs72930369	0.98[EUR][1000 genomes]
rs72930387	1.00[EUR][1000 genomes]
rs72930396	0.98[EUR][1000 genomes]
rs72930400	0.98[EUR][1000 genomes]
rs72932307	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932310	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932311	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932316	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932319	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932336	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932350	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932358	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932364	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932369	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932380	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7562493	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7585722	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7586028	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7604179	0.89[EUR][1000 genomes]
rs7608800	0.80[AMR][1000 genomes];0.89[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
rs60717666	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr2:86677200-86708200	Strong transcription	HepG2	liver
16	chr2:86677200-86709200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:86679400-86708000	Strong transcription	Primary hematopoietic stem cells	blood
18	chr2:86679600-86721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:86679600-86721800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:86680200-86722200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:86681000-86720800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr2:86681600-86722600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr2:86682000-86707000	Strong transcription	Adipose Nuclei	Adipose
26	chr2:86682000-86718600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
29	chr2:86683000-86709600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr2:86683800-86708400	Strong transcription	HMEC	breast
31	chr2:86684000-86720800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:86684000-86726000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr2:86685400-86707000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:86690200-86723200	Strong transcription	Primary B cells from cord blood	blood
35	chr2:86693800-86708000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:86694000-86707000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:86694000-86709000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:86696000-86712000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:86696800-86720600	Strong transcription	Hela-S3	cervix
41	chr2:86697000-86719200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:86697000-86719800	Strong transcription	Thymus	Thymus
43	chr2:86697000-86721200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:86697000-86721400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:86697200-86724600	Strong transcription	Dnd41	blood
46	chr2:86697400-86721000	Strong transcription	HUVEC	blood vessel
47	chr2:86697400-86721600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:86697600-86709600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:86697600-86723000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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