Variant report

Variant	rs3824729
Chromosome Location	chr10:90752616-90752617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:90752453-90754259	GM18505	blood:	n/a	n/a
2	POLR2A	chr10:90749923-90752668	GM12878	blood:	n/a	n/a
3	MYC	chr10:90752475-90753360	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr10:90749504-90754868	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr10:90752372-90754279	GM12878	blood:	n/a	n/a
6	POLR2A	chr10:90752549-90752857	GM12892	blood:	n/a	n/a
7	BCLAF1	chr10:90752509-90753326	GM12878	blood:	n/a	chr10:90752781-90752789
8	POLR2A	chr10:90752522-90754223	GM12891	blood:	n/a	n/a
9	RELA	chr10:90752536-90753364	GM12878	blood:	n/a	chr10:90753123-90753132 chr10:90753123-90753132
10	POLR2A	chr10:90749814-90754387	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:90752533-90754479	GM12892	blood:	n/a	n/a
12	POLR2A	chr10:90752442-90753400	GM12892	blood:	n/a	n/a
13	TBP	chr10:90752480-90754300	GM12878	blood:	n/a	n/a
14	CHD1	chr10:90749926-90754225	GM12878	blood:	n/a	n/a
15	POLR2A	chr10:90749275-90754183	GM19099	blood:	n/a	n/a
16	POLR2A	chr10:90749276-90758032	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr10:90752436-90753474	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:90752569-90752619	Hepatocyte	liver:	n/a
2	chr10:90752569-90752619	AG09309	skin:	n/a
3	chr10:90752569-90752619	HL-60	blood:	n/a
4	chr10:90752569-90752619	AG04450	lung:	fetal
5	chr10:90752569-90752619	HMEC	breast:	n/a
6	chr10:90752569-90752619	HRPEpiC	eye:	n/a
7	chr10:90752569-90752619	NT2-D1	testis:	n/a
8	chr10:90752569-90752619	SAEC	small airway:	n/a
9	chr10:90752569-90752619	HNPCEpiC	eye:	n/a
10	chr10:90752569-90752619	AG10803	skin:	n/a
11	chr10:90752569-90752619	LNCaP	prostate:	n/a
12	chr10:90752569-90752619	NHBE	bronchial:	n/a
13	chr10:90752569-90752619	HIPEpiC	eye:	n/a
14	chr10:90752569-90752619	NB4	blood:	n/a
15	chr10:90752569-90752619	A549	lung:	n/a
16	chr10:90752569-90752619	HRCEpiC	kidney:	n/a
17	chr10:90752569-90752619	PANC-1	pancreas:	n/a
18	chr10:90752569-90752619	GM19239	blood:	n/a
19	chr10:90752569-90752619	HepG2	liver:	n/a
20	chr10:90752569-90752619	SK-N-MC	brain:	n/a
21	chr10:90752569-90752619	RPTEC	kidney:	n/a
22	chr10:90752569-90752619	ovcar-3	ovarian:	n/a
23	chr10:90752569-90752619	GM12891	blood:	n/a
24	chr10:90752569-90752619	HEK293	kidney:	embryo
25	chr10:90752569-90752619	T-47D	breast:	n/a
26	chr10:90752569-90752619	MCF-7	breast:	n/a
27	chr10:90752569-90752619	HUVEC	blood vessel:	n/a
28	chr10:90752569-90752619	HRE	kidney:	n/a
29	chr10:90752569-90752619	GM12878	blood:	n/a
30	chr10:90752569-90752619	U87	brain:	n/a
31	chr10:90752569-90752619	Hela-S3	cervix:	n/a
32	chr10:90752569-90752619	BJ	skin:	n/a
33	chr10:90752569-90752619	K562	blood:	n/a
34	chr10:90752569-90752619	SK-N-SH	brain:	n/a
35	chr10:90752569-90752619	PFSK-1	brain:	n/a
36	chr10:90752569-90752619	AG04449	skin:	fetal
37	chr10:90752569-90752619	Jurkat	blood:	n/a
38	chr10:90752569-90752619	HCM	heart:	n/a
39	chr10:90752569-90752619	HCT-116	colon:	n/a
40	chr10:90752569-90752619	Caco-2	colon:	n/a
41	chr10:90752569-90752619	CMK	blood:	n/a
42	chr10:90752569-90752619	ProgFib	skin:	n/a
43	chr10:90752569-90752619	SKMC	muscle:	n/a
44	chr10:90752569-90752619	GM12892	blood:	n/a
45	chr10:90752569-90752619	IMR90	lung:	fetal
46	chr10:90752569-90752619	AG09319	gingival:	n/a
47	chr10:90752569-90752619	GM06990	blood:	n/a
48	chr10:90752569-90752619	AoSMC	blood vessel:	n/a
49	chr10:90752569-90752619	MCF10A-Er-Src	breast:	n/a
50	chr10:90752569-90752619	ECC-1	luminal epithelium:	n/a

(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
ACTA2	CpG island
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10887877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202918	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12359362	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12775501	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1324551	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571011	0.81[ASN][1000 genomes]
rs1571013	0.81[ASN][1000 genomes]
rs1800682	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1926195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1926196	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926197	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1926199	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1926200	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1926201	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2031610	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3740286	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3758485	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3781204	0.81[ASN][1000 genomes]
rs3824730	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3903454	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4934433	0.84[ASN][1000 genomes]
rs4934434	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6586161	0.85[ASN][1000 genomes]
rs6586163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6586166	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6586167	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7069061	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7069841	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7072828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7076197	0.81[ASN][1000 genomes]
rs7082101	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7082720	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7097467	0.81[ASN][1000 genomes]
rs7097572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897395	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7910660	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7910825	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7911752	0.81[ASN][1000 genomes]
rs7914490	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978522	0.88[AFR][1000 genomes];0.95[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
rs3824729	ACTA2	cis	Whole Blood	GTEx
rs3824729	ACTA2	Cis_1M	lymphoblastoid	RTeQTL
rs3824729	FAS	cis	Muscle Skeletal	GTEx
rs3824729	FAS	cis	Adipose Subcutaneous	GTEx
rs3824729	ACTA2-AS1	cis	Whole Blood	GTEx
rs3824729	ACTA2	cis	multi-tissue	Pritchard
rs3824729	FAS	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90749400-90753400	Active TSS	Left Ventricle	heart
2	chr10:90749400-90754200	Active TSS	Ovary	ovary
3	chr10:90749600-90753600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr10:90749600-90753600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:90749600-90754200	Active TSS	Right Atrium	heart
6	chr10:90749600-90754400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr10:90749600-90755000	Active TSS	GM12878-XiMat	blood
8	chr10:90749800-90753000	Active TSS	Brain Hippocampus Middle	brain
9	chr10:90749800-90753200	Active TSS	HSMMtube	muscle
10	chr10:90749800-90753600	Active TSS	NHDF-Ad	bronchial
11	chr10:90749800-90753800	Active TSS	NHLF	lung
12	chr10:90750000-90752800	Active TSS	Brain Cingulate Gyrus	brain
13	chr10:90750200-90753200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:90750200-90753200	Active TSS	HSMM	muscle
15	chr10:90750200-90753400	Active TSS	Psoas Muscle	Psoas
16	chr10:90750200-90753600	Active TSS	HMEC	breast
17	chr10:90750400-90753000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:90750400-90753800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr10:90751200-90752800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr10:90751200-90753200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr10:90751200-90754000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:90751600-90752800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr10:90751600-90752800	Flanking Active TSS	Liver	Liver
24	chr10:90751600-90753000	Flanking Active TSS	Fetal Lung	lung
25	chr10:90751600-90754200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr10:90751800-90752800	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr10:90751800-90753400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr10:90751800-90754000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:90751800-90754200	Flanking Active TSS	Osteobl	bone
30	chr10:90751800-90755200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:90751800-90768200	Weak transcription	Spleen	Spleen
32	chr10:90752000-90752800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:90752000-90752800	Active TSS	Thymus	Thymus
34	chr10:90752000-90753200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:90752000-90753400	Active TSS	Fetal Thymus	thymus
36	chr10:90752000-90753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr10:90752000-90754000	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr10:90752000-90754200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:90752000-90754200	Active TSS	Stomach Smooth Muscle	stomach
40	chr10:90752000-90754800	Weak transcription	Stomach Mucosa	stomach
41	chr10:90752000-90755200	Weak transcription	Gastric	stomach
42	chr10:90752000-90755200	Weak transcription	Lung	lung
43	chr10:90752000-90755200	Weak transcription	Pancreas	Pancrea
44	chr10:90752000-90761600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:90752000-90770000	Weak transcription	Placenta	Placenta
46	chr10:90752000-90770800	Weak transcription	Esophagus	oesophagus
47	chr10:90752200-90752800	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr10:90752200-90752800	Active TSS	Brain Angular Gyrus	brain
49	chr10:90752200-90752800	Active TSS	Brain Anterior Caudate	brain
50	chr10:90752200-90752800	Active TSS	Pancreatic Islets	Pancreatic Islet

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