Variant report

Variant	rs10509561
Chromosome Location	chr10:90751912-90751913
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:110)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:110 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr10:90751533-90751913	GM12878	blood:	n/a	n/a
2	TEAD4	chr10:90749355-90751985	ECC-1	luminal epithelium:	n/a	n/a
3	SPI1	chr10:90751518-90752048	HL-60	blood:	n/a	n/a
4	YY1	chr10:90751450-90751951	GM12892	blood:	n/a	n/a
5	FOXM1	chr10:90750969-90752006	ECC-1	luminal epithelium:	n/a	n/a
6	BCLAF1	chr10:90749862-90751946	GM12878	blood:	n/a	n/a
7	EBF1	chr10:90750936-90752241	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:90749855-90752124	GM15510	blood:	n/a	n/a
9	BCLAF1	chr10:90750845-90752107	GM12878	blood:	n/a	n/a
10	EP300	chr10:90750895-90751919	GM12878	blood:	n/a	n/a
11	STAT5A	chr10:90750260-90751920	GM12878	blood:	n/a	chr10:90750282-90750294 chr10:90750620-90750628 chr10:90750277-90750289
12	POLR2A	chr10:90749926-90751974	GM12891	blood:	n/a	n/a
13	POLR2A	chr10:90749854-90751934	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr10:90749866-90751970	GM12878	blood:	n/a	n/a
15	PML	chr10:90749912-90752008	GM12878	blood:	n/a	n/a
16	ZBTB33	chr10:90751485-90751964	A549	lung:	n/a	chr10:90751743-90751758
17	POLR2A	chr10:90750038-90752039	GM12891	blood:	n/a	n/a
18	POLR2A	chr10:90749872-90752061	GM12892	blood:	n/a	n/a
19	POLR2A	chr10:90749801-90752335	GM12878	blood:	n/a	n/a
20	TBP	chr10:90750984-90752184	GM12878	blood:	n/a	chr10:90751986-90751997
21	POLR2A	chr10:90749923-90752668	GM12878	blood:	n/a	n/a
22	E2F4	chr10:90750964-90751962	MCF10A-Er-Src	breast:	n/a	n/a
23	ATF2	chr10:90750911-90751984	GM12878	blood:	n/a	n/a
24	MAX	chr10:90749576-90751963	GM12878	blood:	n/a	n/a
25	ZBTB33	chr10:90751553-90751945	GM12878	blood:	n/a	chr10:90751743-90751758
26	POLR2A	chr10:90749923-90752114	GM12892	blood:	n/a	n/a
27	POLR2A	chr10:90749504-90754868	MCF10A-Er-Src	breast:	n/a	n/a
28	RCOR1	chr10:90751620-90751947	HepG2	liver:	n/a	n/a
29	EP300	chr10:90749243-90752016	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr10:90749936-90752305	GM12892	blood:	n/a	n/a
31	POLR2A	chr10:90749941-90751916	Hela-S3	cervix:	n/a	n/a
32	YY1	chr10:90751600-90751996	GM12878	blood:	n/a	n/a
33	MAX	chr10:90749691-90752008	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr10:90750045-90752039	GM12891	blood:	n/a	n/a
35	SMARCC1	chr10:90749457-90751969	Hela-S3	cervix:	n/a	n/a
36	CEBPB	chr10:90751717-90751952	H1-hESC	embryonic stem cell:	n/a	n/a
37	GATA1	chr10:90750096-90752117	PBDE	blood:	n/a	n/a
38	RCOR1	chr10:90749495-90752001	Hela-S3	cervix:	n/a	n/a
39	RELA	chr10:90750925-90751944	GM10847	blood:	n/a	n/a
40	RELA	chr10:90749827-90752219	GM12891	blood:	n/a	n/a
41	CHD2	chr10:90749938-90751986	GM12878	blood:	n/a	n/a
42	RCOR1	chr10:90750856-90752073	GM12878	blood:	n/a	n/a
43	ZNF143	chr10:90751610-90752023	GM12878	blood:	n/a	n/a
44	POLR2A	chr10:90750130-90751933	GM12878	blood:	n/a	n/a
45	NFIC	chr10:90750766-90751913	GM12878	blood:	n/a	n/a
46	GATA3	chr10:90751367-90751998	T-47D	breast:	n/a	n/a
47	STAT1	chr10:90751515-90751934	GM12878	blood:	n/a	n/a
48	YY1	chr10:90751405-90751931	GM12891	blood:	n/a	n/a
49	CTCF	chr10:90751840-90751990	AG09319	gingival:	n/a	n/a
50	SIN3A	chr10:90750255-90752187	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90746474..90748113-chr10:90751872..90754372,2	K562	blood:
2	chr10:90750277..90752970-chr3:42621806..42623827,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACTA2-1	chr10:90751178-90752732	SAF
2	lnc-ACTA2-1	chr10:90751181-90752732	NR_028371
3	lnc-ACTA2-1	chr10:90751179-90752732	NONHSAT015489

No data

Variant related genes	Relation type
ACTA2	TF binding region
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10887875	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202921	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571020	1.00[JPT][hapmap]
rs2147419	0.93[ASN][1000 genomes]
rs2234978	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs4064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085705	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916294	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10509561	FAS	cis	Adipose Subcutaneous	GTEx
rs10509561	ACTA2	cis	Whole Blood	GTEx
rs10509561	FAS	cis	parietal	SCAN
rs10509561	ACTA2	cis	multi-tissue	Pritchard
rs10509561	ACTA2	cis	lymphoblastoid	seeQTL
rs10509561	FAS	cis	multi-tissue	Pritchard
rs10509561	ACTA2-AS1	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90749200-90752200	Active TSS	Brain Substantia Nigra	brain
2	chr10:90749400-90752200	Active TSS	Aorta	Aorta
3	chr10:90749400-90753400	Active TSS	Left Ventricle	heart
4	chr10:90749400-90754200	Active TSS	Ovary	ovary
5	chr10:90749600-90752200	Active TSS	Fetal Intestine Large	intestine
6	chr10:90749600-90752600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:90749600-90753600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:90749600-90753600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:90749600-90754200	Active TSS	Right Atrium	heart
10	chr10:90749600-90754400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr10:90749600-90755000	Active TSS	GM12878-XiMat	blood
12	chr10:90749800-90752000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr10:90749800-90752000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr10:90749800-90752000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr10:90749800-90752000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:90749800-90752000	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr10:90749800-90752400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:90749800-90752400	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr10:90749800-90752400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr10:90749800-90753000	Active TSS	Brain Hippocampus Middle	brain
21	chr10:90749800-90753200	Active TSS	HSMMtube	muscle
22	chr10:90749800-90753600	Active TSS	NHDF-Ad	bronchial
23	chr10:90749800-90753800	Active TSS	NHLF	lung
24	chr10:90750000-90752000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr10:90750000-90752000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr10:90750000-90752000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:90750000-90752000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr10:90750000-90752000	Active TSS	Gastric	stomach
29	chr10:90750000-90752000	Active TSS	Lung	lung
30	chr10:90750000-90752000	Active TSS	Small Intestine	intestine
31	chr10:90750000-90752800	Active TSS	Brain Cingulate Gyrus	brain
32	chr10:90750200-90752000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:90750200-90752000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr10:90750200-90752000	Active TSS	Esophagus	oesophagus
35	chr10:90750200-90752000	Active TSS	Pancreas	Pancrea
36	chr10:90750200-90752000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr10:90750200-90752000	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr10:90750200-90752000	Active TSS	Stomach Mucosa	stomach
39	chr10:90750200-90752200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
40	chr10:90750200-90752200	Active TSS	Right Ventricle	heart
41	chr10:90750200-90752200	Active TSS	A549	lung
42	chr10:90750200-90752400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:90750200-90752400	Active TSS	Muscle Satellite Cultured Cells	--
44	chr10:90750200-90752600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:90750200-90753200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:90750200-90753200	Active TSS	HSMM	muscle
47	chr10:90750200-90753400	Active TSS	Psoas Muscle	Psoas
48	chr10:90750200-90753600	Active TSS	HMEC	breast
49	chr10:90750400-90752000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
50	chr10:90750400-90752000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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