Variant report

Variant	rs7540260
Chromosome Location	chr1:91919533-91919534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11799814	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12060889	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12717797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12758752	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1508586	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1508587	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1876592	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs58884787	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6683272	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6683496	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71668074	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7513482	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7522651	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7526693	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526795	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526972	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7535665	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7542806	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7543080	0.84[EUR][1000 genomes];0.81[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	nsv947496	chr1:91918272-91938103	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7540260	SLC44A3	cis	cerebellum	SCAN
rs7540260	CDC7	cis	Skin Sun Exposed Lower leg	GTEx
rs7540260	CNN3	cis	cerebellum	SCAN
rs7540260	HFM1	cis	cerebellum	SCAN
rs7540260	CDC7	cis	cerebellum	SCAN
rs7540260	CDC7	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91915600-91920000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:91916000-91919600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:91916400-91920800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:91919000-91921600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:91919000-91921600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:91919200-91920200	Enhancers	Fetal Kidney	kidney
7	chr1:91919400-91921200	Enhancers	Fetal Stomach	stomach

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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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