Variant report

Variant	rs4369449
Chromosome Location	chr12:48814369-48814370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10875810	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875815	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2705124	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2705125	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs2731063	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2731092	0.80[CHB][hapmap]
rs2731096	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2731105	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4542454	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4633503	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7139348	0.80[CHB][hapmap]
rs7309958	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7960406	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4369449	C12orf54	cis	lymphoblastoid	seeQTL
rs4369449	C12orf54	cis	multi-tissue	Pritchard
rs4369449	ASB8	cis	parietal	SCAN
rs4369449	RACGAP1	cis	cerebellum	SCAN
rs4369449	COL2A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48808800-48816000	Weak transcription	Ovary	ovary
2	chr12:48812800-48814400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:48812800-48814600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:48813200-48814600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
5	chr12:48813200-48814800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:48813200-48815200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
7	chr12:48813400-48814400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:48813800-48814400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr12:48813800-48814400	Enhancers	Rectal Smooth Muscle	rectum
10	chr12:48814000-48815600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:48814200-48814400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr12:48814200-48814800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr12:48814200-48816000	Weak transcription	Fetal Lung	lung

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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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