Variant report

Variant	rs3750187
Chromosome Location	chr8:105482475-105482476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs12543329	0.94[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12546843	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12550349	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12680920	0.80[ASN][1000 genomes]
rs12681417	0.89[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap]
rs2298840	0.80[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4461873	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap]
rs4474003	0.94[CEU][hapmap];0.94[CHB][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4602859	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510142	0.80[ASN][1000 genomes]
rs66479713	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67403507	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72679133	0.81[EUR][1000 genomes]
rs72679139	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73293244	0.83[ASN][1000 genomes]
rs73295140	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv831417	chr8:105455814-105625608	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3750187	LRP12	cis	cerebellum	SCAN
rs3750187	DCAF13	cis	cerebellum	SCAN
rs3750187	DPYS	cis	cerebellum	SCAN
rs3750187	LRP12	cis	Skin Sun Exposed Lower leg	GTEx
rs3750187	LRP12	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105480600-105483600	Weak transcription	Liver	Liver
2	chr8:105482400-105482600	Bivalent Enhancer	hESC Derived CD184+ Endoderm 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