Variant report

Variant	rs4953625
Chromosome Location	chr2:48977778-48977779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12998409	0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13431355	0.86[CHB][hapmap]
rs4074647	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4074648	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4319975	1.00[MEX][hapmap]
rs4596023	0.91[MEX][hapmap];0.82[YRI][hapmap]
rs4603819	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6722217	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6732424	0.90[ASN][1000 genomes]
rs7563144	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7563465	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9798043	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[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	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4953625	PRKCE	cis	cerebellum	SCAN
rs4953625	LHCGR	cis	Thyroid	GTEx
rs4953625	STON1-GTF2A1L	cis	cerebellum	SCAN
rs4953625	LHCGR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48976600-48980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:48977600-48978800	Enhancers	GM12878-XiMat	blood
3	chr2:48977600-48981400	Weak transcription	Adipose Nuclei	Adipose

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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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