Variant report

Variant	rs62546685
Chromosome Location	chr9:26949822-26949823
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	CHD2	chr9:26949582-26950014	Hela-S3	cervix:	n/a	n/a
2	TAF1	chr9:26949505-26949992	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr9:26949452-26950145	Hela-S3	cervix:	n/a	chr9:26949916-26949927
4	POLR2A	chr9:26949381-26950004	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr9:26949461-26950005	HCT-116	colon:	n/a	n/a
6	POLR2A	chr9:26949373-26950029	MCF10A-Er-Src	breast:	n/a	n/a
7	RCOR1	chr9:26949517-26950165	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr9:26949521-26949986	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr9:26949474-26950009	Hela-S3	cervix:	n/a	n/a
10	MAFK	chr9:26949575-26950016	Hela-S3	cervix:	n/a	n/a
11	GATA3	chr9:26949604-26950107	MCF-7	breast:	n/a	n/a
12	MYC	chr9:26949408-26950009	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr9:26949435-26950008	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr9:26949471-26949923	Hela-S3	cervix:	n/a	n/a
15	NFYA	chr9:26949491-26949955	Hela-S3	cervix:	n/a	n/a
16	EP300	chr9:26949491-26950077	Hela-S3	cervix:	n/a	n/a
17	FOS	chr9:26949438-26950095	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr9:26949628-26950083	Hela-S3	cervix:	n/a	n/a
19	STAT3	chr9:26949457-26949968	MCF10A-Er-Src	breast:	n/a	n/a
20	RCOR1	chr9:26949729-26950021	K562	blood:	n/a	n/a
21	NFYB	chr9:26949508-26949943	Hela-S3	cervix:	n/a	chr9:26949762-26949777
22	TFAP2C	chr9:26949623-26950194	Hela-S3	cervix:	n/a	n/a
23	FOSL1	chr9:26949448-26950131	HCT-116	colon:	n/a	n/a
24	KAP1	chr9:26949054-26950050	HEK293	kidney:	n/a	n/a
25	E2F4	chr9:26949184-26949919	MCF10A-Er-Src	breast:	n/a	n/a
26	TBP	chr9:26949400-26950049	Hela-S3	cervix:	n/a	n/a
27	GATA3	chr9:26949594-26950123	SK-N-SH	brain:	n/a	n/a
28	CEBPB	chr9:26949522-26950114	HCT-116	colon:	n/a	chr9:26949916-26949927
29	FOS	chr9:26949517-26950046	MCF10A-Er-Src	breast:	n/a	n/a
30	NR2F2	chr9:26949627-26950104	MCF-7	breast:	n/a	n/a
31	STAT3	chr9:26949737-26949937	MCF10A-Er-Src	breast:	n/a	n/a
32	CEBPB	chr9:26949672-26950054	IMR90	lung:	n/a	chr9:26949916-26949927
33	JUND	chr9:26949747-26950075	K562	blood:	n/a	n/a
34	RPC155	chr9:26949794-26950579	Hela-S3	cervix:	n/a	n/a
35	USF2	chr9:26949509-26949871	Hela-S3	cervix:	n/a	n/a
36	BRCA1	chr9:26949520-26950094	Hela-S3	cervix:	n/a	n/a
37	STAT3	chr9:26949591-26950081	Hela-S3	cervix:	n/a	n/a
38	MAX	chr9:26949609-26950195	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr9:26949531-26949832	HCT-116	colon:	n/a	n/a
40	JUND	chr9:26949612-26950027	Hela-S3	cervix:	n/a	n/a
41	FOS	chr9:26949478-26950011	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr9:26949401-26949915	U87	brain:	n/a	n/a
43	SETDB1	chr9:26949038-26950063	U2OS	brain:	n/a	n/a
44	CEBPB	chr9:26949692-26950201	K562	blood:	n/a	chr9:26949916-26949927
45	JUN	chr9:26949606-26949988	Hela-S3	cervix:	n/a	n/a
46	CEBPB	chr9:26949413-26950144	HCT-116	colon:	n/a	chr9:26949916-26949927
47	KAP1	chr9:26949524-26950022	U2OS	brain:	n/a	n/a
48	STAT3	chr9:26949514-26949997	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr9:26949458-26950072	Hela-S3	cervix:	n/a	n/a
50	MAX	chr9:26949553-26950099	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PLAA	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10511792	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511794	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511795	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511797	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541145	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910873	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694324	1.00[ASN][1000 genomes]
rs17694499	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694631	0.86[AFR][1000 genomes]
rs17756179	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756299	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184740	0.84[EUR][1000 genomes]
rs3429	0.90[AFR][1000 genomes]
rs57890470	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59100252	1.00[EUR][1000 genomes]
rs59175724	1.00[ASN][1000 genomes]
rs60130669	0.80[AFR][1000 genomes]
rs62542660	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542663	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542665	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542666	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542667	0.95[AFR][1000 genomes]
rs62542669	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542670	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62542672	0.90[AFR][1000 genomes]
rs62542704	0.90[AFR][1000 genomes]
rs62542705	0.86[AFR][1000 genomes]
rs62542706	0.86[AFR][1000 genomes]
rs62542707	0.86[AFR][1000 genomes]
rs62542708	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62544411	1.00[ASN][1000 genomes]
rs62544412	1.00[ASN][1000 genomes]
rs62544413	1.00[ASN][1000 genomes]
rs62544434	1.00[ASN][1000 genomes]
rs62544435	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544437	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544440	1.00[ASN][1000 genomes]
rs62544453	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62546682	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62546683	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018962	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038875	0.80[AFR][1000 genomes]
rs7044910	0.86[EUR][1000 genomes]
rs73433937	0.88[EUR][1000 genomes]
rs73436012	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436044	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436047	0.95[AFR][1000 genomes]
rs73438223	0.90[AFR][1000 genomes]
rs73438278	0.80[AFR][1000 genomes]
rs73438282	0.80[AFR][1000 genomes]
rs73438302	0.80[AFR][1000 genomes]
rs73440204	0.80[AFR][1000 genomes]
rs73440205	0.80[AFR][1000 genomes]
rs73440214	0.80[AFR][1000 genomes]
rs73440217	0.80[AFR][1000 genomes]
rs7865596	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865919	0.80[AFR][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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62546685	CAAP1	cis	Artery Tibial	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26947600-26955200	Weak transcription	Spleen	Spleen
2	chr9:26948000-26955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:26948200-26953600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr9:26948200-26953600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr9:26948200-26954000	Weak transcription	Osteobl	bone
6	chr9:26948200-26955000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:26948200-26955000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:26948200-26955000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:26948200-26955000	Weak transcription	Adipose Nuclei	Adipose
10	chr9:26948200-26955000	Weak transcription	Brain Angular Gyrus	brain
11	chr9:26948200-26955000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:26948200-26955000	Weak transcription	Brain Substantia Nigra	brain
13	chr9:26948200-26955000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:26948200-26955000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:26948200-26955000	Weak transcription	NHDF-Ad	bronchial
16	chr9:26948200-26955000	Weak transcription	NHLF	lung
17	chr9:26948200-26955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:26948200-26955200	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:26948200-26955400	Weak transcription	Psoas Muscle	Psoas
20	chr9:26948200-26955800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:26948400-26950000	Enhancers	HepG2	liver
22	chr9:26948400-26953800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr9:26948400-26954000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:26948400-26954200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:26948400-26954600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:26948400-26955000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:26948400-26955200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr9:26948400-26955200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:26948400-26955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:26948400-26955200	Weak transcription	Liver	Liver
31	chr9:26948800-26950000	Enhancers	HMEC	breast
32	chr9:26949000-26950000	Enhancers	NHEK	skin
33	chr9:26949200-26950600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:26949400-26950000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr9:26949400-26950000	Flanking Active TSS	Hela-S3	cervix
36	chr9:26949600-26950000	Enhancers	Small Intestine	intestine
37	chr9:26949800-26950600	Enhancers	Placenta	Placenta
38	chr9:26949800-26951800	Weak transcription	K562	blood
39	chr9:26949800-26954800	Weak transcription	A549	lung
40	chr9:26949800-26955200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:26949800-26955400	Weak transcription	NH-A	brain

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