Variant report

Variant	rs7097572
Chromosome Location	chr10:90753260-90753261
allele	C/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	chr10:90752994-90753386	GM12891	blood:	n/a	n/a
2	POLR2A	chr10:90752453-90754259	GM18505	blood:	n/a	n/a
3	POLR2A	chr10:90753024-90753371	GM12891	blood:	n/a	n/a
4	MYC	chr10:90752475-90753360	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr10:90749504-90754868	MCF10A-Er-Src	breast:	n/a	n/a
6	RELA	chr10:90752964-90753359	GM12891	blood:	n/a	chr10:90753123-90753132 chr10:90753123-90753132
7	MAFK	chr10:90752900-90753266	IMR90	lung:	n/a	n/a
8	POLR2A	chr10:90752372-90754279	GM12878	blood:	n/a	n/a
9	ZNF384	chr10:90752800-90753275	GM12878	blood:	n/a	n/a
10	ELK1	chr10:90753073-90753309	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:90752974-90753266	GM12891	blood:	n/a	n/a
12	BCLAF1	chr10:90752509-90753326	GM12878	blood:	n/a	chr10:90752781-90752789
13	E2F4	chr10:90752977-90753437	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr10:90752522-90754223	GM12891	blood:	n/a	n/a
15	POLR2A	chr10:90752939-90754470	GM12878	blood:	n/a	n/a
16	RELA	chr10:90752536-90753364	GM12878	blood:	n/a	chr10:90753123-90753132 chr10:90753123-90753132
17	POLR2A	chr10:90752999-90753427	GM12892	blood:	n/a	n/a
18	RELA	chr10:90752891-90753343	GM19099	blood:	n/a	chr10:90753123-90753132 chr10:90753123-90753132
19	FOS	chr10:90752985-90753276	MCF10A-Er-Src	breast:	n/a	n/a
20	WRNIP1	chr10:90752640-90753392	GM12878	blood:	n/a	n/a
21	MYC	chr10:90753004-90753358	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr10:90749814-90754387	GM12878	blood:	n/a	n/a
23	POLR2A	chr10:90752533-90754479	GM12892	blood:	n/a	n/a
24	POLR2A	chr10:90752978-90753456	GM12892	blood:	n/a	n/a
25	POLR2A	chr10:90752442-90753400	GM12892	blood:	n/a	n/a
26	TBP	chr10:90752480-90754300	GM12878	blood:	n/a	n/a
27	CHD1	chr10:90749926-90754225	GM12878	blood:	n/a	n/a
28	POLR2A	chr10:90749275-90754183	GM19099	blood:	n/a	n/a
29	NFYB	chr10:90752891-90753265	GM12878	blood:	n/a	n/a
30	STAT1	chr10:90753161-90753261	GM12878	blood:	n/a	n/a
31	POLR2A	chr10:90749276-90758032	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr10:90752436-90753474	GM12878	blood:	n/a	n/a
33	STAT3	chr10:90753039-90753278	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr10:90752619-90754171	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90746474..90748113-chr10:90751872..90754372,2	K562	blood:

Variant related genes	Relation type
ACTA2	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10887877	1.00[CEU][hapmap];0.90[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1926195	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];0.99[ASN][1000 genomes]
rs1926196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];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]
rs1977389	0.91[JPT][hapmap]
rs2031610	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3740286	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]
rs3752985	0.85[JPT][hapmap]
rs3752986	0.90[JPT][hapmap]
rs3758485	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3781204	0.81[ASN][1000 genomes]
rs3824729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824730	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3903454	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4934433	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs4934434	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6586160	0.86[CHB][hapmap]
rs6586161	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs6586163	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]
rs6586164	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]
rs6586165	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];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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[CHB][hapmap];0.81[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	0.92[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7097572	FAS	cis	parietal	SCAN
rs7097572	FAS	cis	Muscle Skeletal	GTEx
rs7097572	ACTA2	cis	Whole Blood	GTEx
rs7097572	ACTA2	cis	lymphoblastoid	seeQTL
rs7097572	ACTA2	cis	multi-tissue	Pritchard
rs7097572	ACTA2-AS1	cis	Whole Blood	GTEx
rs7097572	FAS	cis	Nerve Tibial	GTEx
rs7097572	FAS	cis	multi-tissue	Pritchard
rs7097572	FAS	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:105 , 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	chr10:90749800-90753600	Active TSS	NHDF-Ad	bronchial
9	chr10:90749800-90753800	Active TSS	NHLF	lung
10	chr10:90750200-90753400	Active TSS	Psoas Muscle	Psoas
11	chr10:90750200-90753600	Active TSS	HMEC	breast
12	chr10:90750400-90753800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:90751200-90754000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr10:90751600-90754200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr10:90751800-90753400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr10:90751800-90754000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr10:90751800-90754200	Flanking Active TSS	Osteobl	bone
18	chr10:90751800-90755200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:90751800-90768200	Weak transcription	Spleen	Spleen
20	chr10:90752000-90753400	Active TSS	Fetal Thymus	thymus
21	chr10:90752000-90753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr10:90752000-90754000	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr10:90752000-90754200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:90752000-90754200	Active TSS	Stomach Smooth Muscle	stomach
25	chr10:90752000-90754800	Weak transcription	Stomach Mucosa	stomach
26	chr10:90752000-90755200	Weak transcription	Gastric	stomach
27	chr10:90752000-90755200	Weak transcription	Lung	lung
28	chr10:90752000-90755200	Weak transcription	Pancreas	Pancrea
29	chr10:90752000-90761600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr10:90752000-90770000	Weak transcription	Placenta	Placenta
31	chr10:90752000-90770800	Weak transcription	Esophagus	oesophagus
32	chr10:90752200-90754000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr10:90752200-90754000	Active TSS	Colonic Mucosa	Colon
34	chr10:90752200-90754000	Active TSS	Rectal Smooth Muscle	rectum
35	chr10:90752200-90754000	Enhancers	A549	lung
36	chr10:90752200-90754000	Enhancers	Dnd41	blood
37	chr10:90752200-90754000	Flanking Active TSS	NHEK	skin
38	chr10:90752200-90754200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr10:90752200-90754400	Enhancers	Primary B cells from peripheral blood	blood
40	chr10:90752200-90755200	Weak transcription	Right Ventricle	heart
41	chr10:90752200-90755800	Weak transcription	Fetal Intestine Large	intestine
42	chr10:90752200-90757200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr10:90752200-90760800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr10:90752200-90768400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr10:90752400-90753400	Enhancers	Primary hematopoietic stem cells	blood
46	chr10:90752400-90753400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr10:90752400-90753400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr10:90752400-90753400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr10:90752400-90754000	Enhancers	Primary T cells from cord blood	blood
50	chr10:90752400-90754000	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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