Variant report

Variant	rs870475
Chromosome Location	chr1:114533394-114533395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11102711	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11580207	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11810241	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402202	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503834	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6689205	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7549714	0.93[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2754686	chr1:114531958-114602958	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs870475	HIPK1	cis	cerebellum	SCAN
rs870475	FAM46C	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114523800-114534600	Weak transcription	Primary T cells from cord blood	blood
2	chr1:114528000-114533400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:114528000-114536600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:114528200-114535800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:114528200-114540800	Weak transcription	Fetal Lung	lung
6	chr1:114530000-114536200	Weak transcription	Fetal Stomach	stomach
7	chr1:114532200-114535800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:114533000-114533600	Enhancers	Fetal Muscle Leg	muscle
9	chr1:114533000-114533800	Enhancers	HSMMtube	muscle

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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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