Variant report

Variant	rs7524900
Chromosome Location	chr1:91915047-91915048
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11164235	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11164236	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11164253	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11164271	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11164309	0.83[AMR][1000 genomes]
rs11164311	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164333	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11164338	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11164343	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11810012	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811919	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135162	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3851270	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3867307	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3867309	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6657350	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7515660	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7515931	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7516032	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7518697	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7523206	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1005574	chr1:91913621-91923934	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
4	esv3503737	chr1:91913728-91916145	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7524900	CNN3	cis	cerebellum	SCAN
rs7524900	CDC7	cis	cerebellum	SCAN
rs7524900	CDC7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91914600-91916000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:91915000-91915600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:91915000-91916000	Enhancers	Fetal Stomach	stomach
4	chr1:91915000-91916400	Enhancers	Hela-S3	cervix

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