Variant report

Variant	rs250723
Chromosome Location	chr5:76056054-76056055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs152778	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs153306	0.97[ASN][1000 genomes]
rs193943	0.88[ASN][1000 genomes]
rs250716	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs250717	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs250719	0.89[ASN][1000 genomes]
rs250720	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs250739	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs250741	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs250742	0.86[ASN][1000 genomes]
rs250744	0.86[ASN][1000 genomes]
rs250745	0.86[ASN][1000 genomes]
rs250746	0.86[ASN][1000 genomes]
rs250747	0.85[ASN][1000 genomes]
rs250748	0.86[ASN][1000 genomes]
rs250750	0.85[ASN][1000 genomes]
rs250751	0.85[ASN][1000 genomes]
rs250752	0.85[ASN][1000 genomes]
rs705402	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs250723	F2RL1	cis	parietal	SCAN
rs250723	F2R	cis	Muscle Skeletal	GTEx
rs250723	DMGDH	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76051000-76056600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:76052400-76056600	Weak transcription	K562	blood
3	chr5:76054200-76056200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:76054400-76056200	Enhancers	HMEC	breast
5	chr5:76054400-76057800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:76054400-76059600	Enhancers	NHEK	skin
7	chr5:76055000-76059000	Weak transcription	HepG2	liver
8	chr5:76055400-76056200	Enhancers	Placenta	Placenta
9	chr5:76055400-76058400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:76055600-76056200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:76056000-76056200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:76056000-76056200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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

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