Variant report

Variant	rs3770058
Chromosome Location	chr2:86710359-86710360
allele	C/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	chr2:86709530-86710455	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:86710121-86711725	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:86709670-86711076	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86708700..86711537-chr2:86718099..86720538,2	MCF-7	breast:
2	chr2:86708605..86710525-chr2:86722087..86724639,2	K562	blood:
3	chr2:86707552..86710497-chr2:86711399..86713123,2	MCF-7	breast:
4	chr2:86666976..86668952-chr2:86708810..86710875,2	K562	blood:

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

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1015117	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10180036	0.84[EUR][1000 genomes]
rs10187880	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1020306	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11127045	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11127046	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1137684	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676576	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684230	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11689330	0.80[AFR][1000 genomes]
rs12614447	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12615285	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12714184	0.84[EUR][1000 genomes]
rs12714186	0.84[EUR][1000 genomes]
rs12714188	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12987172	0.80[AFR][1000 genomes]
rs13015620	0.80[AFR][1000 genomes]
rs13034615	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13390713	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13408041	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13429696	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1465813	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1518807	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241803	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292887	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2367574	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088046	0.81[ASN][1000 genomes]
rs3201448	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731812	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755002	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832040	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832296	0.83[ASN][1000 genomes]
rs4832297	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4832299	0.80[EUR][1000 genomes]
rs4832300	0.80[AFR][1000 genomes]
rs62150269	0.82[EUR][1000 genomes]
rs6725080	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738663	0.80[AFR][1000 genomes]
rs6750226	0.80[AFR][1000 genomes]
rs7369138	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7593151	0.83[ASN][1000 genomes]
rs7596717	0.83[ASN][1000 genomes]
rs8179729	0.83[ASN][1000 genomes]
rs9284788	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs958561	0.84[EUR][1000 genomes]
rs9789777	0.88[ASN][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
rs3770058	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	chr2:86679600-86721400	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	chr2:86696000-86712000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr2:86696800-86720600	Strong transcription	Hela-S3	cervix
31	chr2:86697000-86719200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:86697000-86719800	Strong transcription	Thymus	Thymus
33	chr2:86697000-86721200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:86697000-86721400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:86697200-86724600	Strong transcription	Dnd41	blood
36	chr2:86697400-86721000	Strong transcription	HUVEC	blood vessel
37	chr2:86697400-86721600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:86697600-86723000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:86697800-86714800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
41	chr2:86697800-86721600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood
43	chr2:86698200-86714800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:86698200-86720400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:86699400-86727000	Strong transcription	Placenta	Placenta
46	chr2:86699800-86717000	Strong transcription	Fetal Muscle Leg	muscle
47	chr2:86699800-86718200	Strong transcription	Fetal Stomach	stomach
48	chr2:86699800-86718600	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr2:86699800-86719800	Strong transcription	K562	blood
50	chr2:86700400-86720800	Strong transcription	H1 Cell Line	embryonic stem cell

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