Variant report

Variant	rs250724
Chromosome Location	chr5:76061256-76061257
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs153313	0.84[ASN][1000 genomes]
rs181837	0.82[ASN][1000 genomes]
rs250726	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250727	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250729	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250757	0.84[ASN][1000 genomes]
rs250759	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs253086	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2562514	0.82[ASN][1000 genomes]
rs515362	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv965590	chr5:76061083-76081416	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs250724	DMGDH	cis	cerebellum	SCAN
rs250724	F2R	cis	Muscle Skeletal	GTEx
rs250724	F2RL1	cis	parietal	SCAN
rs250724	F2RL1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76056200-76067000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:76059200-76061400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:76059200-76062600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:76059400-76067400	Weak transcription	HepG2	liver
5	chr5:76059600-76062600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:76059800-76061400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:76060400-76063000	Enhancers	Osteobl	bone
8	chr5:76060600-76061800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:76060600-76070200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:76060800-76061600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:76060800-76063400	Enhancers	NHDF-Ad	bronchial
12	chr5:76061000-76061600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:76061000-76061600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr5:76061000-76061600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr5:76061000-76061600	Enhancers	NH-A	brain
16	chr5:76061200-76061600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:76061200-76062600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

Quick Search:

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

what's new

Quick links