Variant report

Variant	rs62546683
Chromosome Location	chr9:26947918-26947919
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	chr9:26946585-26948232	PBDE	blood:	n/a	n/a
2	POLR2A	chr9:26946947-26948155	K562	blood:	n/a	n/a
3	MAX	chr9:26945575-26948341	NB4	blood:	n/a	n/a
4	POLR2A	chr9:26946668-26948135	HepG2	liver:	n/a	n/a
5	REST	chr9:26945977-26948038	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr9:26945741-26948332	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr9:26946666-26948367	GM19099	blood:	n/a	n/a
8	GATA1	chr9:26945386-26948919	PBDE	blood:	n/a	chr9:26948836-26948857 chr9:26948839-26948850
9	YY1	chr9:26946764-26947923	SK-N-SH	brain:	n/a	chr9:26947900-26947909 chr9:26947119-26947128
10	MAFK	chr9:26947078-26948373	K562	blood:	n/a	chr9:26948146-26948160 chr9:26948148-26948159 chr9:26948147-26948158 chr9:26948148-26948159 chr9:26948147-26948163
11	MXI1	chr9:26946686-26947983	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr9:26946877-26948280	K562	blood:	n/a	n/a
13	POLR2A	chr9:26946725-26948162	GM12892	blood:	n/a	n/a
14	POLR2A	chr9:26946723-26948173	GM19193	blood:	n/a	n/a
15	POLR2A	chr9:26946580-26948280	IMR90	lung:	n/a	n/a
16	TBP	chr9:26946777-26948168	Hela-S3	cervix:	n/a	n/a
17	E2F4	chr9:26946943-26948268	MCF10A-Er-Src	breast:	n/a	chr9:26947900-26947909 chr9:26947560-26947567 chr9:26947122-26947134 chr9:26947560-26947567 chr9:26947560-26947567
18	GABPA	chr9:26946441-26948107	MCF-7	breast:	n/a	chr9:26947474-26947483
19	POLR2A	chr9:26946603-26948012	GM18951	blood:	n/a	n/a
20	POLR2A	chr9:26946769-26948097	MCF-7	breast:	n/a	n/a
21	SRF	chr9:26946823-26948001	HCT-116	colon:	n/a	chr9:26947697-26947710 chr9:26947111-26947121
22	POLR2A	chr9:26945574-26948342	GM12891	blood:	n/a	n/a
23	CHD1	chr9:26945731-26948413	H1-hESC	embryonic stem cell:	n/a	n/a
24	MXI1	chr9:26946587-26948010	IMR90	lung:	n/a	n/a
25	POLR2A	chr9:26945760-26948285	Hela-S3	cervix:	n/a	n/a
26	TAF1	chr9:26946650-26947998	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr9:26946558-26948456	NB4	blood:	n/a	n/a
28	POLR2A	chr9:26946587-26948290	Raji	blood:	n/a	n/a
29	POLR2A	chr9:26947867-26948186	H1-hESC	embryonic stem cell:	n/a	n/a
30	CREB1	chr9:26946823-26948159	GM12878	blood:	n/a	n/a
31	POLR2A	chr9:26946776-26948098	GM18526	blood:	n/a	n/a
32	MXI1	chr9:26946574-26948062	GM12878	blood:	n/a	n/a
33	SIN3A	chr9:26946301-26948088	H1-hESC	embryonic stem cell:	n/a	n/a
34	GABPA	chr9:26946629-26947942	SK-N-SH	brain:	n/a	chr9:26947474-26947483
35	POLR2A	chr9:26946335-26948319	GM12878	blood:	n/a	n/a
36	CHD1	chr9:26946870-26948168	GM12878	blood:	n/a	n/a
37	POLR2A	chr9:26946366-26948187	MCF10A-Er-Src	breast:	n/a	n/a
38	FOXA1	chr9:26947725-26948214	HepG2	liver:	n/a	n/a
39	CTCF	chr9:26946787-26947986	K562	blood:	n/a	chr9:26947138-26947146
40	MAZ	chr9:26946018-26948128	IMR90	lung:	n/a	n/a
41	SIN3AK20	chr9:26946608-26947959	MCF-7	breast:	n/a	n/a
42	MYC	chr9:26945612-26948147	NB4	blood:	n/a	n/a
43	ATF1	chr9:26947031-26947971	K562	blood:	n/a	n/a
44	POLR2A	chr9:26946834-26948241	GM12878	blood:	n/a	n/a
45	POLR2A	chr9:26946545-26948037	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr9:26946593-26948269	SK-N-MC	brain:	n/a	n/a
47	MYC	chr9:26946763-26947996	K562	blood:	n/a	n/a
48	POLR2A	chr9:26946614-26948018	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr9:26946750-26948119	GM15510	blood:	n/a	n/a
50	FOXA1	chr9:26947792-26948066	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:47894333..47895242-chr9:26947215..26948074,2	NB4	blood:
2	chr9:26891080..26894676-chr9:26945695..26949113,9	K562	blood:
3	chr9:26891080..26895841-chr9:26945501..26948974,8	K562	blood:
4	chr9:26890485..26893190-chr9:26945159..26948755,7	MCF-7	breast:
5	chr9:26943098..26949574-chr9:26949927..26957421,13	K562	blood:
6	chr9:26890972..26893985-chr9:26945405..26948624,3	MCF-7	breast:
7	chr9:26945881..26949167-chr9:26974909..26976838,3	MCF-7	breast:
8	chr9:26947507..26949074-chr9:26950532..26952059,2	MCF-7	breast:
9	chr9:26891961..26892542-chr9:26947832..26948665,2	K562	blood:
10	chr9:26920077..26923896-chr9:26945076..26948067,5	MCF-7	breast:

Variant related genes	Relation type
PLAA	TF binding region
ENSG00000124201	Chromatin interaction
ENSG00000096872	Chromatin interaction
ENSG00000234676	Chromatin interaction
ENSG00000240306	Chromatin interaction
ENSG00000137055	Chromatin interaction
ENSG00000120159	Chromatin interaction
ENSG00000177410	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10511792	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511795	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511797	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541145	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	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756179	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756299	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184740	0.84[EUR][1000 genomes]
rs57890470	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59100252	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59175724	1.00[ASN][1000 genomes]
rs62542660	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542663	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542665	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542666	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542669	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542670	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62542708	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62546685	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]
rs7044910	0.86[EUR][1000 genomes]
rs73433937	0.88[EUR][1000 genomes]
rs73436012	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436044	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865596	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	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
rs62546683	CAAP1	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26940000-26948400	Active TSS	GM12878-XiMat	blood
2	chr9:26944600-26948400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr9:26944800-26948000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:26945200-26948000	Active TSS	NHLF	lung
5	chr9:26945200-26948200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:26945200-26948200	Active TSS	K562	blood
7	chr9:26945200-26948400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr9:26945200-26948400	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr9:26945400-26948000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr9:26945400-26948200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr9:26945600-26948200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr9:26945600-26948200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:26945600-26948200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:26945600-26948200	Active TSS	Right Atrium	heart
15	chr9:26945600-26948400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr9:26945600-26948400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:26945800-26948000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:26945800-26948000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:26945800-26948000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:26945800-26948000	Active TSS	Fetal Muscle Trunk	muscle
21	chr9:26945800-26948000	Active TSS	Left Ventricle	heart
22	chr9:26945800-26948000	Active TSS	Lung	lung
23	chr9:26945800-26948000	Active TSS	Ovary	ovary
24	chr9:26945800-26948000	Active TSS	Pancreas	Pancrea
25	chr9:26945800-26948000	Active TSS	Right Ventricle	heart
26	chr9:26945800-26948000	Active TSS	HSMM	muscle
27	chr9:26945800-26948200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:26945800-26948200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:26945800-26948200	Active TSS	Fetal Kidney	kidney
30	chr9:26945800-26948200	Active TSS	Psoas Muscle	Psoas
31	chr9:26945800-26948400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:26946000-26948000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:26946000-26948000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:26946000-26948000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:26946000-26948000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:26946000-26948000	Active TSS	Aorta	Aorta
37	chr9:26946000-26948000	Active TSS	NHDF-Ad	bronchial
38	chr9:26946000-26948200	Active TSS	Colonic Mucosa	Colon
39	chr9:26946000-26948400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:26946000-26948400	Active TSS	A549	lung
41	chr9:26946200-26948000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:26946200-26948000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:26946200-26948000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:26946200-26948000	Active TSS	Colon Smooth Muscle	Colon
45	chr9:26946200-26948000	Active TSS	Fetal Intestine Large	intestine
46	chr9:26946200-26948000	Active TSS	Placenta Amnion	Placenta Amnion
47	chr9:26946200-26948000	Active TSS	Dnd41	blood
48	chr9:26946200-26948000	Active TSS	Hela-S3	cervix
49	chr9:26946200-26948000	Active TSS	HSMMtube	muscle
50	chr9:26946200-26948200	Active TSS	Pancreatic Islets	Pancreatic Islet

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