Variant report

Variant	rs13103368
Chromosome Location	chr4:175528022-175528023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10866372	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11133047	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11133048	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11133049	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11722219	0.82[ASN][1000 genomes]
rs11725394	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11728575	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11733443	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11932191	0.87[ASN][1000 genomes]
rs12647899	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12649430	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12649779	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12650961	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13130070	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13130669	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1820525	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2555652	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34618616	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4695934	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1018390	chr4:175475505-175969742	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv880403	chr4:175485318-175535392	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv880679	chr4:175502088-175552622	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv880584	chr4:175505749-175644689	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv880497	chr4:175513812-175556222	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13103368	HPGD	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175525600-175528600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:175525800-175528200	Weak transcription	K562	blood
3	chr4:175526000-175528200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:175526600-175528200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:175526600-175529800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr4:175527000-175528600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr4:175527000-175530000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr4:175527200-175528200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr4:175527600-175529400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:175527800-175529800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr4:175528000-175528200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:175528000-175528400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr4:175528000-175529000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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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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