Variant report

Variant	rs9793489
Chromosome Location	chr1:224397459-224397460
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224394938..224397843-chr1:224400035..224402726,3	K562	blood:
2	chr1:224371208..224373580-chr1:224396360..224399111,2	K562	blood:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction
ENSG00000232628	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2011117	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2176600	0.83[AMR][1000 genomes]
rs4653568	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653569	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4654000	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4654003	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6669401	0.83[AMR][1000 genomes]
rs6678942	0.82[AMR][1000 genomes]
rs6681673	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682292	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs908801	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][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	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9793489	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs9793489	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs9793489	FBXO28	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224391600-224400000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:224391600-224400200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:224391600-224407000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:224392600-224400400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:224393400-224399000	Weak transcription	Brain Germinal Matrix	brain
7	chr1:224393600-224397600	Weak transcription	Left Ventricle	heart
8	chr1:224393600-224397600	Weak transcription	Spleen	Spleen
9	chr1:224393600-224397800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:224393600-224397800	Weak transcription	Right Ventricle	heart
11	chr1:224393600-224398800	Weak transcription	Brain Substantia Nigra	brain
12	chr1:224393600-224398800	Weak transcription	Fetal Kidney	kidney
13	chr1:224393600-224399000	Weak transcription	Brain Anterior Caudate	brain
14	chr1:224393600-224399000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:224393600-224399000	Weak transcription	Psoas Muscle	Psoas
16	chr1:224393600-224399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:224393600-224399200	Weak transcription	Lung	lung
18	chr1:224393600-224400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:224393600-224400200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:224393600-224400200	Weak transcription	Gastric	stomach
21	chr1:224393600-224400400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:224393600-224400400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:224393600-224400800	Weak transcription	Right Atrium	heart
24	chr1:224393600-224401200	Weak transcription	Esophagus	oesophagus
25	chr1:224393600-224401200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:224393800-224397800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:224393800-224398000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:224393800-224398000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:224393800-224398600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:224393800-224398800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:224393800-224398800	Weak transcription	Fetal Heart	heart
32	chr1:224393800-224398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:224393800-224398800	Weak transcription	Fetal Lung	lung
34	chr1:224393800-224398800	Weak transcription	Fetal Stomach	stomach
35	chr1:224393800-224399000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:224393800-224399000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:224393800-224399000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:224393800-224399000	Weak transcription	NH-A	brain
39	chr1:224393800-224399200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:224393800-224400200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:224393800-224400200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:224393800-224400200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:224393800-224400200	Weak transcription	HSMMtube	muscle
44	chr1:224393800-224405600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
46	chr1:224394000-224398800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:224394000-224398800	Weak transcription	A549	lung
48	chr1:224394000-224398800	Weak transcription	NHEK	skin
49	chr1:224394000-224399000	Weak transcription	HUVEC	blood vessel
50	chr1:224394000-224399000	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links