Variant report

Variant	rs4239225
Chromosome Location	chr17:38127112-38127113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000108344	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000265666	Chromatin interaction
ENSG00000167914	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs3859191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3859192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3859193	0.89[AFR][1000 genomes]
rs3907022	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4065876	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4580194	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56030650	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56326707	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60134943	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60137005	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4239225	GSDMA	cis	Esophagus Muscularis	GTEx
rs4239225	GSDMA	cis	Thyroid	GTEx
rs4239225	GSDMA	cis	Nerve Tibial	GTEx
rs4239225	GSDMA	cis	lung	GTEx
rs4239225	GSDMA	cis	Adipose Subcutaneous	GTEx
rs4239225	MED24	cis	Nerve Tibial	GTEx
rs4239225	GSDMA	cis	Artery Aorta	GTEx
rs4239225	MED24	cis	Artery Tibial	GTEx
rs4239225	GSDMA	cis	Artery Tibial	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38110800-38128800	Weak transcription	Gastric	stomach
2	chr17:38122200-38130600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:38122200-38130600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr17:38124000-38128000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr17:38124000-38129600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:38124000-38134600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:38124800-38127600	Enhancers	Fetal Intestine Small	intestine
8	chr17:38125000-38127200	Enhancers	Duodenum Mucosa	Duodenum
9	chr17:38125000-38127200	Enhancers	Fetal Intestine Large	intestine
10	chr17:38125200-38128400	Weak transcription	Primary B cells from cord blood	blood
11	chr17:38125400-38128000	Enhancers	Colonic Mucosa	Colon
12	chr17:38126200-38127800	Enhancers	Placenta	Placenta
13	chr17:38126400-38128000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr17:38126600-38127600	Enhancers	Esophagus	oesophagus
15	chr17:38126600-38127600	Enhancers	Lung	lung
16	chr17:38126600-38127600	Enhancers	K562	blood
17	chr17:38126800-38128000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr17:38127000-38128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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