Variant report

Variant	rs304483
Chromosome Location	chr10:91158237-91158238
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	NR3C1	chr10:91157727-91158356	A549	lung:	n/a	n/a
2	FOXA2	chr10:91157833-91158309	A549	lung:	n/a	n/a
3	KAP1	chr10:91157939-91158465	HEK293	kidney:	n/a	n/a
4	NR3C1	chr10:91157672-91158261	A549	lung:	n/a	n/a
5	NR3C1	chr10:91157743-91158290	A549	lung:	n/a	n/a
6	TCF12	chr10:91157586-91158281	A549	lung:	n/a	n/a
7	FOXA1	chr10:91157837-91158265	HepG2	liver:	n/a	n/a
8	SP1	chr10:91157868-91158264	HepG2	liver:	n/a	n/a
9	HEY1	chr10:91158127-91158312	HepG2	liver:	n/a	n/a
10	FOXA2	chr10:91157793-91158381	A549	lung:	n/a	n/a
11	SETDB1	chr10:91157850-91158716	U2OS	brain:	n/a	n/a
12	NR3C1	chr10:91157842-91158238	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91157615..91160495-chr10:91173578..91176122,3	MCF-7	breast:

Variant related genes	Relation type
IFIT1	TF binding region
ENSG00000107798	Chromatin interaction
ENSG00000152778	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10159774	0.82[AMR][1000 genomes]
rs10749607	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs215493	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2458877	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2484045	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs303170	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs303172	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303174	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs303217	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs304439	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs304440	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs304443	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs304448	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs304449	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304451	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs304478	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs304485	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304494	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs304495	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs304504	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs305371	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs305373	0.82[AMR][1000 genomes]
rs305375	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs305376	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs305377	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4934475	0.82[AMR][1000 genomes]
rs559198	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs627524	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	esv34085	chr10:91065949-91174175	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs304483	IFIT5	cis	Artery Tibial	GTEx
rs304483	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs304483	IFIT5	cis	Skin Sun Exposed Lower leg	GTEx
rs304483	IFIT5	cis	Nerve Tibial	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91152800-91173600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:91152800-91174000	Weak transcription	Gastric	stomach
3	chr10:91153000-91164200	Weak transcription	Esophagus	oesophagus
4	chr10:91153200-91162000	Weak transcription	HSMM	muscle
5	chr10:91153200-91163800	Weak transcription	Spleen	Spleen
6	chr10:91153200-91173600	Weak transcription	Brain Germinal Matrix	brain
7	chr10:91153400-91162200	Weak transcription	Placenta	Placenta
8	chr10:91153400-91162200	Weak transcription	Lung	lung
9	chr10:91153400-91163400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr10:91153400-91164000	Weak transcription	Pancreas	Pancrea
11	chr10:91153400-91172400	Weak transcription	Thymus	Thymus
12	chr10:91153600-91162200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr10:91153600-91162200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:91153600-91165400	Weak transcription	Fetal Thymus	thymus
15	chr10:91153600-91173600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr10:91154000-91162200	Weak transcription	Primary T cells from cord blood	blood
17	chr10:91154000-91162200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr10:91154000-91162200	Weak transcription	Fetal Stomach	stomach
19	chr10:91154000-91162400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:91154000-91164200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr10:91154000-91166800	Weak transcription	Right Ventricle	heart
22	chr10:91154200-91161800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr10:91154200-91162000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr10:91154200-91162200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:91154200-91162200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr10:91154200-91162200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr10:91154200-91164000	Weak transcription	Right Atrium	heart
28	chr10:91154200-91172400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr10:91154200-91173200	Weak transcription	Primary B cells from cord blood	blood
30	chr10:91154200-91173400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr10:91154200-91173400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:91154600-91162200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr10:91154600-91173000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr10:91154800-91159400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr10:91154800-91163400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr10:91155200-91161800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr10:91155200-91162200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:91155200-91162200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr10:91155200-91162200	Weak transcription	Aorta	Aorta
40	chr10:91155200-91162200	Weak transcription	Brain Anterior Caudate	brain
41	chr10:91155200-91162200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr10:91155200-91162200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:91155200-91164000	Weak transcription	Brain Angular Gyrus	brain
44	chr10:91155200-91173200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr10:91155400-91159400	Weak transcription	Ovary	ovary
46	chr10:91155400-91162000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr10:91155400-91162200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr10:91155400-91162200	Weak transcription	Brain Hippocampus Middle	brain
49	chr10:91155400-91162200	Weak transcription	Brain Substantia Nigra	brain
50	chr10:91155400-91162200	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links