Variant report

Variant	rs7089558
Chromosome Location	chr10:90781152-90781153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10887882	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10887883	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12775232	0.86[ASN][1000 genomes]
rs1571019	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1810763	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1977389	0.85[ASN][1000 genomes]
rs2031612	0.85[ASN][1000 genomes]
rs2296600	0.85[ASN][1000 genomes]
rs2862833	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35150762	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752985	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3752986	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3781202	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7095466	0.86[ASN][1000 genomes]
rs7096473	0.87[ASN][1000 genomes]
rs7901656	0.85[ASN][1000 genomes]
rs7910435	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs913043	0.85[AFR][1000 genomes];0.87[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7089558	FAS	cis	Muscle Skeletal	GTEx
rs7089558	FAS	cis	Adipose Subcutaneous	GTEx
rs7089558	ACTA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90754000-90789600	Weak transcription	A549	lung
2	chr10:90756200-90781800	Weak transcription	Stomach Mucosa	stomach
3	chr10:90761800-90783800	Weak transcription	Gastric	stomach
4	chr10:90761800-90786200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr10:90762400-90785800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr10:90762600-90786000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr10:90762800-90782000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr10:90766200-90785600	Strong transcription	GM12878-XiMat	blood
9	chr10:90767600-90786600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr10:90767800-90781800	Weak transcription	Small Intestine	intestine
11	chr10:90768400-90785000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:90769400-90781400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr10:90771600-90782600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr10:90771600-90784800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr10:90771600-90789600	Weak transcription	Brain Anterior Caudate	brain
16	chr10:90771800-90808600	Weak transcription	Primary T cells from cord blood	blood
17	chr10:90772400-90795000	Weak transcription	Placenta	Placenta
18	chr10:90772600-90784600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr10:90772600-90789600	Weak transcription	Fetal Stomach	stomach
20	chr10:90772600-90791800	Weak transcription	Esophagus	oesophagus
21	chr10:90772600-90792000	Weak transcription	Colonic Mucosa	Colon
22	chr10:90772600-90795800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr10:90774400-90781200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr10:90774600-90784800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:90774800-90781600	Strong transcription	Ovary	ovary
26	chr10:90775000-90789400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr10:90775200-90789400	Weak transcription	NH-A	brain
28	chr10:90776200-90789400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr10:90776600-90781400	Weak transcription	Pancreas	Pancrea
30	chr10:90776600-90792600	Weak transcription	Right Ventricle	heart
31	chr10:90776800-90789400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr10:90777800-90781400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr10:90778000-90791200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:90778800-90781200	Strong transcription	NHDF-Ad	bronchial
35	chr10:90779200-90791600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:90779400-90781200	ZNF genes & repeats	Fetal Thymus	thymus
37	chr10:90779600-90781400	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr10:90780200-90785200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:90780200-90791400	Weak transcription	Spleen	Spleen
40	chr10:90780400-90781400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:90780400-90784600	Weak transcription	Thymus	Thymus
42	chr10:90780400-90786400	Weak transcription	Fetal Brain Male	brain
43	chr10:90780400-90789600	Weak transcription	Colon Smooth Muscle	Colon
44	chr10:90780400-90790600	Weak transcription	Hela-S3	cervix
45	chr10:90780600-90781200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr10:90780600-90781800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr10:90780600-90782200	Weak transcription	HMEC	breast
48	chr10:90780600-90782200	Weak transcription	NHEK	skin
49	chr10:90780600-90785000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr10:90780600-90786400	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links