Variant report

Variant	rs1926200
Chromosome Location	chr10:90746533-90746534
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	RAD21	chr10:90746519-90747157	ECC-1	luminal epithelium:	n/a	chr10:90746901-90746910 chr10:90746895-90746914
2	SPI1	chr10:90746297-90746606	GM12878	blood:	n/a	n/a
3	RUNX3	chr10:90746210-90747652	GM12878	blood:	n/a	n/a
4	CTCF	chr10:90746420-90746570	AG04449	skin:	n/a	n/a
5	RUNX3	chr10:90746237-90746666	GM12878	blood:	n/a	n/a
6	CTCF	chr10:90746460-90746610	SK-N-SH_RA	brain:	n/a	n/a
7	SPI1	chr10:90746207-90746710	HL-60	blood:	n/a	n/a
8	EGR1	chr10:90746254-90746573	GM12878	blood:	n/a	n/a
9	RAD21	chr10:90745871-90747254	SK-N-SH	brain:	n/a	chr10:90746901-90746910 chr10:90746895-90746914
10	EGR1	chr10:90746283-90746540	GM12878	blood:	n/a	n/a
11	SMC3	chr10:90746504-90747572	GM12878	blood:	n/a	chr10:90746899-90746913
12	CTCF	chr10:90746500-90746650	NHLF	lung:	n/a	n/a
13	POLR2A	chr10:90746213-90746749	SK-N-MC	brain:	n/a	n/a
14	SMC3	chr10:90746473-90747400	SK-N-SH	brain:	n/a	chr10:90746899-90746913
15	USF2	chr10:90746414-90746708	GM12878	blood:	n/a	n/a
16	SPI1	chr10:90746260-90746561	HL-60	blood:	n/a	n/a
17	CTCF	chr10:90746520-90746670	HPF	lung:	n/a	n/a
18	TBP	chr10:90746513-90746537	K562	blood:	n/a	n/a
19	ATF2	chr10:90746533-90747189	GM12878	blood:	n/a	n/a
20	SPI1	chr10:90746305-90746640	GM12891	blood:	n/a	n/a
21	NFIC	chr10:90746221-90746732	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:90694289..90695530-chr10:90746407..90747396,8	K562	blood:
2	chr10:90746474..90748113-chr10:90751872..90754372,2	K562	blood:
3	chr10:90694284..90695841-chr10:90746413..90747615,9	MCF-7	breast:
4	chr10:90694253..90695800-chr10:90745177..90747385,25	MCF-7	breast:
5	chr10:90732274..90733956-chr10:90744737..90747226,2	K562	blood:

Variant related genes	Relation type
FAS	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10788624	0.81[ASN][1000 genomes]
rs10887876	0.81[ASN][1000 genomes]
rs10887877	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11202918	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12359362	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12775501	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1324551	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1800682	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926195	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1926196	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1926197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031610	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3740286	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3758485	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3824729	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3824730	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3903454	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4934433	0.86[ASN][1000 genomes]
rs4934434	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6586160	0.82[ASN][1000 genomes]
rs6586161	0.87[ASN][1000 genomes]
rs6586163	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6586164	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6586165	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6586166	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6586167	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7069061	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7069841	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7072828	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7082101	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7082720	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7097572	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7897395	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7910660	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7910825	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7914490	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978522	0.90[AFR][1000 genomes];0.98[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1926200	FAS	cis	Muscle Skeletal	GTEx
rs1926200	FAS	cis	Esophagus Muscularis	GTEx
rs1926200	FAS	cis	Nerve Tibial	GTEx
rs1926200	ACTA2	cis	multi-tissue	Pritchard
rs1926200	FAS	cis	Adipose Subcutaneous	GTEx
rs1926200	ACTA2-AS1	cis	Whole Blood	GTEx
rs1926200	ACTA2	cis	Whole Blood	GTEx
rs1926200	ACTA2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90735200-90749800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr10:90735600-90748600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr10:90735600-90749200	Weak transcription	Fetal Muscle Leg	muscle
4	chr10:90735600-90749200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr10:90738200-90747800	Enhancers	Colon Smooth Muscle	Colon
6	chr10:90739400-90749400	Weak transcription	NHEK	skin
7	chr10:90739600-90747200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr10:90739600-90748600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr10:90739600-90749000	Weak transcription	Adipose Nuclei	Adipose
10	chr10:90739600-90749200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:90739800-90749200	Weak transcription	HMEC	breast
12	chr10:90740200-90749200	Weak transcription	Left Ventricle	heart
13	chr10:90740800-90749200	Weak transcription	NH-A	brain
14	chr10:90741000-90747200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:90741000-90747400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr10:90741000-90749200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:90741000-90749400	Weak transcription	Spleen	Spleen
18	chr10:90741600-90749200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:90741600-90749200	Weak transcription	Psoas Muscle	Psoas
20	chr10:90741600-90749400	Weak transcription	HSMM	muscle
21	chr10:90742800-90747200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr10:90742800-90749800	Weak transcription	Brain Hippocampus Middle	brain
23	chr10:90743000-90746600	Weak transcription	Liver	Liver
24	chr10:90743200-90746600	Enhancers	Stomach Smooth Muscle	stomach
25	chr10:90743600-90746600	Enhancers	Ovary	ovary
26	chr10:90743800-90746800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr10:90743800-90749600	Weak transcription	Fetal Intestine Large	intestine
28	chr10:90744200-90749200	Weak transcription	Fetal Stomach	stomach
29	chr10:90744200-90749200	Weak transcription	Right Atrium	heart
30	chr10:90744200-90749600	Weak transcription	Fetal Intestine Small	intestine
31	chr10:90744200-90750000	Weak transcription	Small Intestine	intestine
32	chr10:90744600-90748400	Weak transcription	Osteobl	bone
33	chr10:90744600-90750000	Weak transcription	Stomach Mucosa	stomach
34	chr10:90745000-90748200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr10:90745000-90749600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:90745200-90746800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:90745200-90749200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:90745400-90747400	Enhancers	Rectal Smooth Muscle	rectum
39	chr10:90745600-90747200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr10:90745600-90749200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:90745600-90749200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr10:90745600-90750000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr10:90745800-90747200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:90746000-90746600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr10:90746000-90746600	Enhancers	NHLF	lung
46	chr10:90746000-90747400	Genic enhancers	Fetal Lung	lung
47	chr10:90746200-90746800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
48	chr10:90746200-90746800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
49	chr10:90746200-90746800	Active TSS	Aorta	Aorta
50	chr10:90746200-90747200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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