Variant report

Variant	rs2131252
Chromosome Location	chr4:167460285-167460286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10000903	0.95[EUR][1000 genomes]
rs10034660	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10034776	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1492527	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492528	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492536	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1492538	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4691291	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4691292	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6536968	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844841	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7658687	0.96[ASN][1000 genomes]
rs7670136	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs970765	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9992574	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034421	chr4:166961339-167893289	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv537339	chr4:166961339-167893289	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv881405	chr4:167193885-167628013	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1023051	chr4:167304814-168211540	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv537340	chr4:167304814-168211540	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv881309	chr4:167377133-167500233	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv830143	chr4:167386232-167538014	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1017028	chr4:167420519-167697787	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1035039	chr4:167455577-167521841	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv596065	chr4:167460285-167490086	Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2131252	C4orf39	cis	parietal	SCAN
rs2131252	TRIM60	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:167459200-167460800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:167459600-167460400	Enhancers	H9 Cell Line	embryonic stem cell
3	chr4:167459600-167460400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:167459800-167460400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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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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