Variant report

Variant	rs3740286
Chromosome Location	chr10:90751340-90751341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:184)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:184 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:90749843-90751568	U87	brain:	n/a	n/a
2	TEAD4	chr10:90749355-90751985	ECC-1	luminal epithelium:	n/a	n/a
3	HEY1	chr10:90750767-90751661	HepG2	liver:	n/a	n/a
4	SIN3AK20	chr10:90751340-90751654	HepG2	liver:	n/a	n/a
5	TAF1	chr10:90750968-90751506	GM12891	blood:	n/a	n/a
6	FOXM1	chr10:90750969-90752006	ECC-1	luminal epithelium:	n/a	n/a
7	CUX1	chr10:90751101-90751503	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:90749915-90751407	HL-60	blood:	n/a	n/a
9	BCLAF1	chr10:90749862-90751946	GM12878	blood:	n/a	n/a
10	EBF1	chr10:90750936-90752241	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:90749855-90752124	GM15510	blood:	n/a	n/a
12	SIN3AK20	chr10:90750110-90751867	PANC-1	pancreas:	n/a	n/a
13	EP300	chr10:90750009-90751464	SK-N-SH	brain:	n/a	n/a
14	BCLAF1	chr10:90750845-90752107	GM12878	blood:	n/a	n/a
15	EP300	chr10:90750895-90751919	GM12878	blood:	n/a	n/a
16	TBP	chr10:90750999-90751879	Hela-S3	cervix:	n/a	n/a
17	STAT5A	chr10:90750260-90751920	GM12878	blood:	n/a	chr10:90750282-90750294 chr10:90750620-90750628 chr10:90750277-90750289
18	FOXM1	chr10:90750426-90751824	GM12878	blood:	n/a	n/a
19	POLR2A	chr10:90749926-90751974	GM12891	blood:	n/a	n/a
20	POLR2A	chr10:90749854-90751934	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr10:90749866-90751970	GM12878	blood:	n/a	n/a
22	PML	chr10:90749912-90752008	GM12878	blood:	n/a	n/a
23	POLR2A	chr10:90750038-90752039	GM12891	blood:	n/a	n/a
24	TCF12	chr10:90749391-90751818	ECC-1	luminal epithelium:	n/a	chr10:90750157-90750167
25	POLR2A	chr10:90749872-90752061	GM12892	blood:	n/a	n/a
26	MXI1	chr10:90749572-90751342	Hela-S3	cervix:	n/a	n/a
27	FOS	chr10:90751030-90751372	MCF10A-Er-Src	breast:	n/a	n/a
28	MAX	chr10:90749410-90751872	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr10:90749801-90752335	GM12878	blood:	n/a	n/a
30	TBP	chr10:90750984-90752184	GM12878	blood:	n/a	chr10:90751986-90751997
31	POLR2A	chr10:90749923-90752668	GM12878	blood:	n/a	n/a
32	POLR2A	chr10:90749949-90751434	HL-60	blood:	n/a	n/a
33	SMC3	chr10:90751057-90751370	GM12878	blood:	n/a	n/a
34	E2F4	chr10:90750964-90751962	MCF10A-Er-Src	breast:	n/a	n/a
35	CTBP2	chr10:90750029-90751845	H1-hESC	embryonic stem cell:	n/a	n/a
36	HA-E2F1	chr10:90750046-90751876	MCF-7	breast:	n/a	n/a
37	SMARCB1	chr10:90749936-90751664	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr10:90749839-90751807	Hela-S3	cervix:	n/a	n/a
39	TAF1	chr10:90750882-90751384	GM12892	blood:	n/a	n/a
40	REST	chr10:90749980-90751440	HL-60	blood:	n/a	chr10:90750302-90750316 chr10:90750541-90750554
41	YY1	chr10:90751028-90751401	GM12891	blood:	n/a	n/a
42	ATF2	chr10:90750911-90751984	GM12878	blood:	n/a	n/a
43	MAX	chr10:90749576-90751963	GM12878	blood:	n/a	n/a
44	YY1	chr10:90750941-90751345	GM12878	blood:	n/a	n/a
45	POLR2A	chr10:90749923-90752114	GM12892	blood:	n/a	n/a
46	POLR2A	chr10:90749504-90754868	MCF10A-Er-Src	breast:	n/a	n/a
47	EP300	chr10:90749243-90752016	ECC-1	luminal epithelium:	n/a	n/a
48	ZBTB7A	chr10:90749920-90751398	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr10:90750146-90751426	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr10:90749936-90752305	GM12892	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:90750740..90751472-chr19:6530793..6531570,2	Hela-S3	cervix:
2	chr10:90639301..90642051-chr10:90749823..90751899,2	MCF-7	breast:
3	chr10:90750277..90752970-chr3:42621806..42623827,2	MCF-7	breast:
4	chr10:90750826..90751525-chr15:65588108..65588850,2	Hela-S3	cervix:

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAMBPL1-1	chr10:90751045-90751383	NONHSAT015488
2	lnc-ACTA2-1	chr10:90751178-90752732	SAF
3	lnc-STAMBPL1-1	chr10:90751185-90751383	NONHSAT015490
4	lnc-STAMBPL1-1	chr10:90751188-90751383	NONHSAT015491
5	lnc-STAMBPL1-1	chr10:90751200-90751383	NONHSAT015492
6	lnc-STAMBPL1-1	chr10:90751205-90751383	NONHSAT015493
7	lnc-ACTA2-1	chr10:90751181-90752732	NR_028371
8	lnc-ACTA2-1	chr10:90751179-90752732	NONHSAT015489

No data

Variant related genes	Relation type
ACTA2	TF binding region
ENSG00000199568	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000138134	Chromatin interaction
ENSG00000125657	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10887877	0.90[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	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[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[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.96[ASN][1000 genomes]
rs1926195	1.00[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[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.85[MKK][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]
rs3752985	0.90[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]
rs3824730	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]
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];0.88[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4934434	0.91[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][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	0.86[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs6586161	0.91[CHB][hapmap];0.84[CHD][hapmap];0.84[ASN][1000 genomes]
rs6586163	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6586164	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6586165	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6586166	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6586167	1.00[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[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.85[MKK][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];0.90[JPT][hapmap];0.90[LWK][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3740286	ACTA2	cis	lymphoblastoid	seeQTL
rs3740286	FAS	cis	Nerve Tibial	GTEx
rs3740286	ACTA2-AS1	cis	Whole Blood	GTEx
rs3740286	FAS	cis	parietal	SCAN
rs3740286	FAS	cis	Adipose Subcutaneous	GTEx
rs3740286	ACTA2	Cis_1M	lymphoblastoid	RTeQTL
rs3740286	ACTA2	cis	Whole Blood	GTEx
rs3740286	LIPK	cis	cerebellum	SCAN
rs3740286	FAS	cis	Muscle Skeletal	GTEx
rs3740286	ACTA2	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 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	chr10:90749600-90751800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr10:90749600-90752200	Active TSS	Fetal Intestine Large	intestine
7	chr10:90749600-90752600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:90749600-90753600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr10:90749600-90753600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr10:90749600-90754200	Active TSS	Right Atrium	heart
11	chr10:90749600-90754400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr10:90749600-90755000	Active TSS	GM12878-XiMat	blood
13	chr10:90749800-90751600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr10:90749800-90751800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr10:90749800-90751800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr10:90749800-90751800	Active TSS	Fetal Kidney	kidney
17	chr10:90749800-90751800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr10:90749800-90752000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
19	chr10:90749800-90752000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:90749800-90752000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr10:90749800-90752000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:90749800-90752000	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr10:90749800-90752400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:90749800-90752400	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr10:90749800-90752400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr10:90749800-90753000	Active TSS	Brain Hippocampus Middle	brain
27	chr10:90749800-90753200	Active TSS	HSMMtube	muscle
28	chr10:90749800-90753600	Active TSS	NHDF-Ad	bronchial
29	chr10:90749800-90753800	Active TSS	NHLF	lung
30	chr10:90750000-90751600	Bivalent/Poised TSS	Fetal Brain Female	brain
31	chr10:90750000-90751600	Active TSS	Placenta Amnion	Placenta Amnion
32	chr10:90750000-90751600	Active TSS	Rectal Smooth Muscle	rectum
33	chr10:90750000-90751600	Active TSS	Thymus	Thymus
34	chr10:90750000-90751800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr10:90750000-90751800	Active TSS	Brain Anterior Caudate	brain
36	chr10:90750000-90751800	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr10:90750000-90751800	Active TSS	Fetal Heart	heart
38	chr10:90750000-90752000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr10:90750000-90752000	Active TSS	H9 Cell Line	embryonic stem cell
40	chr10:90750000-90752000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr10:90750000-90752000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr10:90750000-90752000	Active TSS	Gastric	stomach
43	chr10:90750000-90752000	Active TSS	Lung	lung
44	chr10:90750000-90752000	Active TSS	Small Intestine	intestine
45	chr10:90750000-90752800	Active TSS	Brain Cingulate Gyrus	brain
46	chr10:90750200-90751600	Active TSS	Colon Smooth Muscle	Colon
47	chr10:90750200-90751600	Active TSS	Fetal Intestine Small	intestine
48	chr10:90750200-90751600	Active TSS	Fetal Lung	lung
49	chr10:90750200-90751600	Active TSS	Fetal Muscle Leg	muscle
50	chr10:90750200-90751600	Bivalent/Poised TSS	HepG2	liver

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