Variant report

Variant	rs7662488
Chromosome Location	chr4:20661344-20661345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10031524	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs10938803	0.80[CHB][hapmap];0.85[CHD][hapmap];0.87[MEX][hapmap]
rs11936560	0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs1820505	0.81[ASN][1000 genomes]
rs2114474	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs3816874	0.87[CHB][hapmap]
rs4577580	0.81[ASN][1000 genomes]
rs6447971	0.81[ASN][1000 genomes]
rs6447972	0.81[ASN][1000 genomes]
rs6447973	0.81[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs6857386	0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs7668797	0.81[ASN][1000 genomes]
rs7688592	0.93[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7689421	0.91[MEX][hapmap]
rs7694208	0.83[MEX][hapmap]
rs964019	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829875	chr4:20502895-20680956	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	89 gene(s)	inside rSNPs	diseases
2	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7662488	PACRGL	cis	lung	GTEx
rs7662488	C4orf28	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20654600-20673800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:20659600-20661400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr4:20659600-20661400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:20659600-20661400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr4:20659800-20661400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:20660000-20663800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:20660000-20674000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:20660200-20664200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:20660400-20663800	Weak transcription	HMEC	breast
10	chr4:20660600-20663800	Weak transcription	NHEK	skin
11	chr4:20660600-20664200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:20661200-20661400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:20661200-20661400	Enhancers	Placenta Amnion	Placenta Amnion

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