Variant report

Variant	rs2292418
Chromosome Location	chr1:220445488-220445489
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	CEBPB	chr1:220445441-220446101	K562	blood:	n/a	n/a
2	POLR2A	chr1:220444744-220446443	H1-hESC	embryonic stem cell:	n/a	n/a
3	ETS1	chr1:220445473-220446010	K562	blood:	n/a	chr1:220445799-220445808 chr1:220445799-220445808 chr1:220445797-220445806 chr1:220445798-220445807 chr1:220445795-220445811
4	POLR2A	chr1:220445429-220446315	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr1:220445328-220446194	MCF-7	breast:	n/a	n/a
6	MAX	chr1:220445028-220446277	NB4	blood:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
7	HCFC1	chr1:220444935-220446420	K562	blood:	n/a	n/a
8	YY1	chr1:220445436-220446139	GM12878	blood:	n/a	chr1:220445899-220445908
9	POLR2A	chr1:220445404-220446257	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:220445103-220446147	H1-hESC	embryonic stem cell:	n/a	n/a
11	CREB1	chr1:220445281-220446213	H1-hESC	embryonic stem cell:	n/a	n/a
12	STAT5A	chr1:220445295-220446199	K562	blood:	n/a	n/a
13	SPI1	chr1:220445403-220445800	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:220444840-220446403	PFSK-1	brain:	n/a	n/a
15	CREB1	chr1:220445365-220446103	A549	lung:	n/a	n/a
16	POLR2A	chr1:220444876-220446303	GM12878	blood:	n/a	n/a
17	SIN3A	chr1:220445485-220446336	GM12878	blood:	n/a	chr1:220445888-220445897 chr1:220445886-220445895
18	NFIC	chr1:220445463-220446383	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr1:220445058-220446215	GM12878	blood:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
20	USF1	chr1:220445222-220446329	HCT-116	colon:	n/a	chr1:220445899-220445915 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445881-220445902 chr1:220445888-220445897 chr1:220445887-220445896 chr1:220445885-220445896 chr1:220445886-220445895
21	FOXP2	chr1:220445245-220446026	PFSK-1	brain:	n/a	n/a
22	HEY1	chr1:220444982-220446186	K562	blood:	n/a	chr1:220445901-220445916
23	MYC	chr1:220445321-220446145	H1-hESC	embryonic stem cell:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
24	POLR2A	chr1:220444974-220446141	K562	blood:	n/a	n/a
25	RUNX3	chr1:220444964-220446132	GM12878	blood:	n/a	n/a
26	STAT5A	chr1:220444817-220446222	GM12878	blood:	n/a	chr1:220445273-220445285
27	MAZ	chr1:220445191-220446060	HepG2	liver:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
28	TAF1	chr1:220445483-220446178	K562	blood:	n/a	n/a
29	MAX	chr1:220444984-220446325	SK-N-SH	brain:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
30	ELF1	chr1:220445359-220446070	K562	blood:	n/a	chr1:220445798-220445807 chr1:220445795-220445808 chr1:220445512-220445524
31	POLR2A	chr1:220445434-220446344	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr1:220445314-220446206	GM12891	blood:	n/a	n/a
33	POLR2A	chr1:220445455-220446289	HEK293	kidney:	n/a	n/a
34	NFYB	chr1:220445447-220446062	GM12878	blood:	n/a	n/a
35	MAX	chr1:220445327-220446208	MCF-7	breast:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
36	POLR2A	chr1:220444909-220446477	GM12878	blood:	n/a	n/a
37	SMC3	chr1:220445443-220446105	GM12878	blood:	n/a	chr1:220445473-220445483
38	POLR2A	chr1:220444777-220446366	MCF10A-Er-Src	breast:	n/a	n/a
39	REST	chr1:220445438-220446098	K562	blood:	n/a	chr1:220445467-220445480 chr1:220445854-220445867 chr1:220445854-220445867
40	HCFC1	chr1:220444541-220446530	Hela-S3	cervix:	n/a	n/a
41	GABPA	chr1:220445192-220446286	MCF-7	breast:	n/a	chr1:220445871-220445880 chr1:220445838-220445852 chr1:220445841-220445852 chr1:220445841-220445855 chr1:220445841-220445850
42	GABPA	chr1:220445414-220446118	HL-60	blood:	n/a	chr1:220445871-220445880 chr1:220445838-220445852 chr1:220445841-220445852 chr1:220445841-220445855 chr1:220445841-220445850
43	ATF3	chr1:220445443-220445972	A549	lung:	n/a	chr1:220445887-220445896 chr1:220445876-220445896 chr1:220445871-220445880 chr1:220445887-220445907
44	TAF1	chr1:220445441-220446101	H1-neurons	neurons:	n/a	n/a
45	ZKSCAN1	chr1:220445156-220445994	Hela-S3	cervix:	n/a	n/a
46	USF2	chr1:220445065-220446325	GM12878	blood:	n/a	chr1:220445899-220445915 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445881-220445902 chr1:220445888-220445897 chr1:220445887-220445896 chr1:220445885-220445896 chr1:220445146-220445157 chr1:220445886-220445895
47	POLR2A	chr1:220443180-220446565	GM12891	blood:	n/a	n/a
48	CHD2	chr1:220445115-220446483	K562	blood:	n/a	n/a
49	RUNX3	chr1:220445461-220446248	GM12878	blood:	n/a	n/a
50	BHLHE40	chr1:220445414-220446198	HepG2	liver:	n/a	chr1:220445899-220445915 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445881-220445902 chr1:220445888-220445897 chr1:220445887-220445896 chr1:220445886-220445895

No.	Distal block	Cell Line	Cell type
1	chr1:220440528..220443413-chr1:220443546..220445862,4	MCF-7	breast:
2	chr1:220445189..220446035-chr17:56736253..56736785,2	Hela-S3	cervix:
3	chr1:220443657..220445570-chr1:220960265..220962335,2	MCF-7	breast:
4	chr1:220445319..220445878-chr21:48055351..48056081,2	Hela-S3	cervix:
5	chr1:28975066..28975586-chr1:220445322..220446174,2	NB4	blood:

Variant related genes	Relation type
AURKAPS1	TF binding region
ENSG00000202077	Chromatin interaction
ENSG00000160310	Chromatin interaction
ENSG00000213033	Chromatin interaction
ENSG00000270103	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1059140	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11547779	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12032345	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2289189	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2289191	0.91[AMR][1000 genomes]
rs3767655	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41303055	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[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	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2292418	RAB3GAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220443600-220446600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:220443800-220446000	Active TSS	GM12878-XiMat	blood
3	chr1:220443800-220446600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr1:220444000-220445600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:220444000-220446000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr1:220444000-220446600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:220444000-220446600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:220444200-220446200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:220444200-220446400	Active TSS	HSMMtube	muscle
10	chr1:220444200-220446600	Active TSS	Muscle Satellite Cultured Cells	--
11	chr1:220444400-220446200	Active TSS	Primary T cells fromperipheralblood	blood
12	chr1:220444400-220446400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:220444400-220446400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:220444400-220446400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:220444400-220446400	Active TSS	Colonic Mucosa	Colon
16	chr1:220444400-220446400	Active TSS	Fetal Intestine Small	intestine
17	chr1:220444400-220446600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:220444400-220446600	Active TSS	Brain Angular Gyrus	brain
19	chr1:220444600-220445600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr1:220444600-220446000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr1:220444600-220446000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:220444600-220446000	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr1:220444600-220446000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr1:220444600-220446000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:220444600-220446000	Active TSS	HMEC	breast
26	chr1:220444600-220446000	Active TSS	K562	blood
27	chr1:220444600-220446000	Active TSS	NHLF	lung
28	chr1:220444600-220446200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:220444600-220446200	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr1:220444600-220446200	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr1:220444600-220446200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:220444600-220446200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:220444600-220446200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:220444600-220446200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:220444600-220446200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr1:220444600-220446200	Active TSS	Fetal Brain Female	brain
37	chr1:220444600-220446200	Active TSS	Fetal Kidney	kidney
38	chr1:220444600-220446400	Active TSS	H9 Cell Line	embryonic stem cell
39	chr1:220444600-220446400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:220444600-220446400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:220444600-220446400	Active TSS	Fetal Intestine Large	intestine
42	chr1:220444600-220446400	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr1:220444600-220446400	Active TSS	Right Ventricle	heart
44	chr1:220444600-220446400	Active TSS	Stomach Mucosa	stomach
45	chr1:220444600-220446400	Active TSS	A549	lung
46	chr1:220444600-220446400	Active TSS	HSMM	muscle
47	chr1:220444600-220446600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:220444600-220446600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:220444600-220446600	Active TSS	Brain Cingulate Gyrus	brain
50	chr1:220444600-220446600	Active TSS	Brain Hippocampus Middle	brain

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