Variant report

Variant	rs3824730
Chromosome Location	chr10:90752128-90752129
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr10:90750936-90752241	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:90749801-90752335	GM12878	blood:	n/a	n/a
3	TBP	chr10:90750984-90752184	GM12878	blood:	n/a	chr10:90751986-90751997
4	POLR2A	chr10:90749923-90752668	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:90749504-90754868	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr10:90749936-90752305	GM12892	blood:	n/a	n/a
7	RELA	chr10:90749827-90752219	GM12891	blood:	n/a	n/a
8	SIN3A	chr10:90750255-90752187	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:90749903-90752253	GM12892	blood:	n/a	n/a
10	RELA	chr10:90750078-90752154	GM12878	blood:	n/a	n/a
11	RELA	chr10:90750996-90752207	GM18505	blood:	n/a	n/a
12	STAT3	chr10:90751023-90752140	GM12878	blood:	n/a	n/a
13	MTA3	chr10:90749765-90752142	GM12878	blood:	n/a	n/a
14	POLR2A	chr10:90749814-90754387	GM12878	blood:	n/a	n/a
15	POLR2A	chr10:90749946-90752242	Raji	blood:	n/a	n/a
16	WRNIP1	chr10:90749898-90752258	GM12878	blood:	n/a	n/a
17	MXI1	chr10:90749866-90752238	GM12878	blood:	n/a	n/a
18	CHD1	chr10:90749926-90754225	GM12878	blood:	n/a	n/a
19	EP300	chr10:90751962-90752137	K562	blood:	n/a	n/a
20	POLR2A	chr10:90749275-90754183	GM19099	blood:	n/a	n/a
21	POLR2A	chr10:90749226-90752314	GM12891	blood:	n/a	n/a
22	POLR2A	chr10:90749276-90758032	MCF10A-Er-Src	breast:	n/a	n/a
23	RELA	chr10:90749819-90752149	GM15510	blood:	n/a	n/a
24	POLR2A	chr10:90749800-90752338	GM12878	blood:	n/a	n/a
25	STAT3	chr10:90751944-90752171	MCF10A-Er-Src	breast:	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
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10887877	0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11202918	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12359362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775501	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1324551	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1571011	0.81[ASN][1000 genomes]
rs1571013	0.81[ASN][1000 genomes]
rs1800682	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1926195	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1926196	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1926197	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1926199	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1926200	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1926201	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1977389	0.95[JPT][hapmap]
rs2031610	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3740286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752985	0.91[JPT][hapmap]
rs3752986	0.95[JPT][hapmap]
rs3758485	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781204	0.81[ASN][1000 genomes]
rs3824729	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3903454	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4934433	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs4934434	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6586160	0.87[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs6586161	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs6586163	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6586164	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6586165	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6586166	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6586167	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7069061	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7069841	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7072828	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7076197	0.81[ASN][1000 genomes]
rs7082101	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7082720	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7097467	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs7097572	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7897395	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7910660	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7910825	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7911752	0.81[ASN][1000 genomes]
rs7914490	0.96[ASN][1000 genomes]
rs978522	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[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
rs3824730	FAS	cis	Adipose Subcutaneous	GTEx
rs3824730	FAS	cis	Nerve Tibial	GTEx
rs3824730	ACTA2-AS1	cis	Whole Blood	GTEx
rs3824730	ACTA2	cis	multi-tissue	Pritchard
rs3824730	ACTA2	Cis_1M	lymphoblastoid	RTeQTL
rs3824730	ACTA2	cis	Whole Blood	GTEx
rs3824730	FAS	cis	Muscle Skeletal	GTEx

Chromatin state (count:114 , 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	chr10:90749800-90752400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:90749800-90752400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr10:90749800-90752400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr10:90749800-90753000	Active TSS	Brain Hippocampus Middle	brain
16	chr10:90749800-90753200	Active TSS	HSMMtube	muscle
17	chr10:90749800-90753600	Active TSS	NHDF-Ad	bronchial
18	chr10:90749800-90753800	Active TSS	NHLF	lung
19	chr10:90750000-90752800	Active TSS	Brain Cingulate Gyrus	brain
20	chr10:90750200-90752200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
21	chr10:90750200-90752200	Active TSS	Right Ventricle	heart
22	chr10:90750200-90752200	Active TSS	A549	lung
23	chr10:90750200-90752400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:90750200-90752400	Active TSS	Muscle Satellite Cultured Cells	--
25	chr10:90750200-90752600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:90750200-90753200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr10:90750200-90753200	Active TSS	HSMM	muscle
28	chr10:90750200-90753400	Active TSS	Psoas Muscle	Psoas
29	chr10:90750200-90753600	Active TSS	HMEC	breast
30	chr10:90750400-90752200	Active TSS	Fetal Muscle Trunk	muscle
31	chr10:90750400-90752200	Active TSS	NHEK	skin
32	chr10:90750400-90752600	Active TSS	Primary T cells fromperipheralblood	blood
33	chr10:90750400-90753000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:90750400-90753800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr10:90751200-90752800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:90751200-90753200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:90751200-90754000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr10:90751400-90752400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr10:90751600-90752200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:90751600-90752200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr10:90751600-90752200	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr10:90751600-90752200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr10:90751600-90752200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr10:90751600-90752200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr10:90751600-90752200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr10:90751600-90752200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:90751600-90752200	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr10:90751600-90752200	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr10:90751600-90752200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr10:90751600-90752200	Flanking Active TSS	Fetal Muscle Leg	muscle

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