Variant report

Variant	rs5753298
Chromosome Location	chr22:31128763-31128764
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	chr22:31124952..31127381-chr22:31127811..31130663,2	K562	blood:
2	chr22:31063275..31065151-chr22:31126656..31129232,2	K562	blood:

Variant related genes	Relation type
ENSG00000167065	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11913875	0.82[ASN][1000 genomes]
rs12483846	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12484930	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs136337	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs136339	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs136343	0.83[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs136344	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs136345	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs136351	0.84[ASN][1000 genomes]
rs136354	0.82[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs136355	0.84[ASN][1000 genomes]
rs136356	0.81[ASN][1000 genomes]
rs136380	0.87[ASN][1000 genomes]
rs136383	0.85[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs136388	0.83[ASN][1000 genomes]
rs4820899	0.85[ASN][1000 genomes]
rs55765123	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5749156	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5749157	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5749161	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs5753281	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs5753285	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5753287	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5753290	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5753292	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs5753294	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5753295	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5753297	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5753299	0.80[ASN][1000 genomes]
rs5753300	0.84[ASN][1000 genomes]
rs58467547	0.82[AMR][1000 genomes]
rs5997737	0.83[ASN][1000 genomes]
rs61537428	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62235882	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62235892	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7292017	0.82[ASN][1000 genomes]
rs8184976	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs909705	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs926340	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5753298	SEC14L2	cis	cerebellum	SCAN
rs5753298	XBP1	cis	cerebellum	SCAN
rs5753298	PES1	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31113800-31132800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr22:31114000-31140600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr22:31115200-31128800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr22:31115400-31128800	Weak transcription	NHDF-Ad	bronchial
5	chr22:31115600-31149400	Weak transcription	Brain Hippocampus Middle	brain
6	chr22:31117000-31140200	Weak transcription	Pancreas	Pancrea
7	chr22:31118400-31138600	Weak transcription	Fetal Brain Female	brain
8	chr22:31123000-31137200	Weak transcription	Gastric	stomach
9	chr22:31123600-31131200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr22:31125400-31131200	Weak transcription	Fetal Intestine Small	intestine
11	chr22:31126200-31130600	Enhancers	HUVEC	blood vessel
12	chr22:31126400-31129800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr22:31126600-31128800	Weak transcription	NH-A	brain
14	chr22:31126600-31129200	Weak transcription	GM12878-XiMat	blood
15	chr22:31126600-31136200	Weak transcription	K562	blood
16	chr22:31127400-31128800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr22:31127600-31129400	Enhancers	Spleen	Spleen
18	chr22:31127800-31128800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr22:31128000-31129000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr22:31128200-31139600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr22:31128400-31129000	Enhancers	Brain Substantia Nigra	brain
22	chr22:31128600-31128800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr22:31128600-31128800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr22:31128600-31129000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr22:31128600-31129000	Enhancers	Brain Angular Gyrus	brain
26	chr22:31128600-31129000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr22:31128600-31129200	Enhancers	Brain Cingulate Gyrus	brain
28	chr22:31128600-31129400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr22:31128600-31129400	Enhancers	Brain Anterior Caudate	brain
30	chr22:31128600-31129800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr22:31128600-31129800	Enhancers	HSMM	muscle
32	chr22:31128600-31130000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links