Variant report

Variant	rs7524281
Chromosome Location	chr1:152783255-152783256
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1048535	0.95[CEU][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs10494277	0.82[CEU][hapmap]
rs11578927	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs11586156	0.82[CEU][hapmap]
rs11587012	0.91[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs12094874	0.94[EUR][1000 genomes]
rs12239774	0.82[CEU][hapmap]
rs12725760	0.85[CEU][hapmap]
rs1412548	0.82[CEU][hapmap]
rs1591077	0.82[CEU][hapmap]
rs1930127	0.87[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs2339381	0.82[CEU][hapmap]
rs41268484	0.90[EUR][1000 genomes]
rs4539140	0.82[CEU][hapmap]
rs4845482	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs56130300	0.81[EUR][1000 genomes]
rs6587706	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv428521	chr1:152663153-152831578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv947325	chr1:152670204-152793272	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
10	nsv508615	chr1:152724155-152787503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv1799675	chr1:152759643-152785456	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1010346	chr1:152761911-152787707	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv1012943	chr1:152762750-152787707	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	nsv1009885	chr1:152762750-152851273	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7524281	LCE1E	cis	uninvolved skin	skin_eQTL
rs7524281	SMCP	cis	cerebellum	SCAN
rs7524281	LCE1E	cis	lesional skin	skin_eQTL
rs7524281	LCE1D	cis	Skin Sun Exposed Lower leg	GTEx
rs7524281	LCE1E	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152779400-152783600	Weak transcription	Esophagus	oesophagus
2	chr1:152779600-152783400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:152779600-152783400	Weak transcription	HMEC	breast
4	chr1:152779600-152783600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:152783000-152784200	Enhancers	NHEK	skin
6	chr1:152783200-152784400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:152783200-152784400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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