Variant report

Variant	rs978522
Chromosome Location	chr10:90748338-90748339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90694789..90695368-chr10:90747585..90748463,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10887877	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11202918	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12359362	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12775501	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1324551	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1800682	0.98[ASN][1000 genomes]
rs1926195	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1926196	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1926197	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1926199	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1926200	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1926201	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2031610	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740286	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3758485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3824729	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3824730	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3903454	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4934433	0.86[ASN][1000 genomes]
rs4934434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6586160	0.82[ASN][1000 genomes]
rs6586161	0.85[ASN][1000 genomes]
rs6586163	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6586164	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6586165	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6586166	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6586167	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7069061	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7069841	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7072828	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7082101	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7082720	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7097572	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7897395	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7910660	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7910825	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7914490	0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs978522	FAS	cis	Nerve Tibial	GTEx
rs978522	FAS	cis	Muscle Skeletal	GTEx
rs978522	ACTA2	cis	multi-tissue	Pritchard
rs978522	FAS	cis	Adipose Subcutaneous	GTEx
rs978522	ACTA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 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	chr10:90739400-90749400	Weak transcription	NHEK	skin
6	chr10:90739600-90748600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr10:90739600-90749000	Weak transcription	Adipose Nuclei	Adipose
8	chr10:90739600-90749200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:90739800-90749200	Weak transcription	HMEC	breast
10	chr10:90740200-90749200	Weak transcription	Left Ventricle	heart
11	chr10:90740800-90749200	Weak transcription	NH-A	brain
12	chr10:90741000-90749200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr10:90741000-90749400	Weak transcription	Spleen	Spleen
14	chr10:90741600-90749200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr10:90741600-90749200	Weak transcription	Psoas Muscle	Psoas
16	chr10:90741600-90749400	Weak transcription	HSMM	muscle
17	chr10:90742800-90749800	Weak transcription	Brain Hippocampus Middle	brain
18	chr10:90743800-90749600	Weak transcription	Fetal Intestine Large	intestine
19	chr10:90744200-90749200	Weak transcription	Fetal Stomach	stomach
20	chr10:90744200-90749200	Weak transcription	Right Atrium	heart
21	chr10:90744200-90749600	Weak transcription	Fetal Intestine Small	intestine
22	chr10:90744200-90750000	Weak transcription	Small Intestine	intestine
23	chr10:90744600-90748400	Weak transcription	Osteobl	bone
24	chr10:90744600-90750000	Weak transcription	Stomach Mucosa	stomach
25	chr10:90745000-90749600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:90745200-90749200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr10:90745600-90749200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:90745600-90749200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr10:90745600-90750000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr10:90746200-90748400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:90746400-90749200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr10:90746400-90749800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:90746400-90749800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:90746600-90748600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr10:90746600-90748600	Weak transcription	HepG2	liver
36	chr10:90746600-90748800	Weak transcription	NHDF-Ad	bronchial
37	chr10:90746600-90749200	Weak transcription	Fetal Kidney	kidney
38	chr10:90746600-90749200	Weak transcription	Ovary	ovary
39	chr10:90746600-90749600	Enhancers	Liver	Liver
40	chr10:90746600-90749800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr10:90746800-90749000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr10:90746800-90749200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr10:90746800-90749200	Weak transcription	Aorta	Aorta
44	chr10:90746800-90749800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:90747000-90749600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr10:90747000-90749800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr10:90747000-90750000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr10:90747000-90750000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr10:90747200-90748800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr10:90747200-90749200	Enhancers	Primary neutrophils fromperipheralblood	blood

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