Variant report

Variant	rs7072828
Chromosome Location	chr10:90754953-90754954
allele	G/T
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	chr10:90754865-90755809	GM12892	blood:	n/a	n/a
2	POLR2A	chr10:90754907-90755211	GM12892	blood:	n/a	n/a
3	POLR2A	chr10:90754915-90755835	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:90754895-90755299	GM12892	blood:	n/a	n/a
5	POLR2A	chr10:90754863-90756068	GM12878	blood:	n/a	n/a
6	POLR2A	chr10:90754865-90755210	GM12892	blood:	n/a	n/a
7	TBP	chr10:90754869-90755203	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:90754951-90755665	Raji	blood:	n/a	n/a
9	POLR2A	chr10:90749276-90758032	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ACTA2	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10887877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202918	0.85[AFR][1000 genomes];0.93[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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800682	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1926195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1926196	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1926197	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1926199	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1926200	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1926201	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[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	0.80[ASN][1000 genomes]
rs3824729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3824730	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3903454	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4934433	0.83[ASN][1000 genomes]
rs4934434	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6586161	0.84[ASN][1000 genomes]
rs6586163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6586164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6586165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586166	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6586167	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7069061	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069841	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7076197	0.80[ASN][1000 genomes]
rs7082101	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7082720	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7097467	0.80[ASN][1000 genomes]
rs7097572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7897395	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910660	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7910825	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7914490	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs978522	0.88[AFR][1000 genomes];0.94[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
rs7072828	FAS	cis	Muscle Skeletal	GTEx
rs7072828	ACTA2	cis	multi-tissue	Pritchard
rs7072828	FAS	cis	Nerve Tibial	GTEx
rs7072828	ACTA2	Cis_1M	lymphoblastoid	RTeQTL
rs7072828	FAS	cis	Adipose Subcutaneous	GTEx
rs7072828	ACTA2	cis	Whole Blood	GTEx
rs7072828	ACTA2-AS1	cis	Whole Blood	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90749600-90755000	Active TSS	GM12878-XiMat	blood
2	chr10:90751800-90755200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:90751800-90768200	Weak transcription	Spleen	Spleen
4	chr10:90752000-90755200	Weak transcription	Gastric	stomach
5	chr10:90752000-90755200	Weak transcription	Lung	lung
6	chr10:90752000-90755200	Weak transcription	Pancreas	Pancrea
7	chr10:90752000-90761600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:90752000-90770000	Weak transcription	Placenta	Placenta
9	chr10:90752000-90770800	Weak transcription	Esophagus	oesophagus
10	chr10:90752200-90755200	Weak transcription	Right Ventricle	heart
11	chr10:90752200-90755800	Weak transcription	Fetal Intestine Large	intestine
12	chr10:90752200-90757200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr10:90752200-90760800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr10:90752200-90768400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr10:90752800-90755000	Weak transcription	Thymus	Thymus
16	chr10:90752800-90773400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr10:90753000-90755000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr10:90753000-90758600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr10:90753000-90761400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr10:90753400-90755000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr10:90753400-90755000	Weak transcription	Fetal Thymus	thymus
22	chr10:90753400-90755200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:90753400-90755200	Weak transcription	Left Ventricle	heart
24	chr10:90753400-90755200	Weak transcription	Psoas Muscle	Psoas
25	chr10:90753400-90755200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr10:90753400-90756400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr10:90753400-90756600	Weak transcription	Primary B cells from cord blood	blood
28	chr10:90753400-90761600	Weak transcription	Aorta	Aorta
29	chr10:90753800-90760400	Weak transcription	Brain Anterior Caudate	brain
30	chr10:90754000-90755000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr10:90754000-90755000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:90754000-90755000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr10:90754000-90755000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr10:90754000-90755200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:90754000-90755200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:90754000-90755200	Weak transcription	Adipose Nuclei	Adipose
37	chr10:90754000-90755200	Weak transcription	Colonic Mucosa	Colon
38	chr10:90754000-90755200	Weak transcription	Fetal Lung	lung
39	chr10:90754000-90755200	Weak transcription	Small Intestine	intestine
40	chr10:90754000-90755600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:90754000-90755800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:90754000-90755800	Enhancers	NHEK	skin
43	chr10:90754000-90756600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:90754000-90759000	Weak transcription	HSMMtube	muscle
45	chr10:90754000-90760400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:90754000-90760800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:90754000-90761000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr10:90754000-90761000	Weak transcription	Colon Smooth Muscle	Colon
49	chr10:90754000-90761200	Weak transcription	NH-A	brain
50	chr10:90754000-90779400	Weak transcription	HepG2	liver

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