Variant report

Variant	rs8024062
Chromosome Location	chr15:58595129-58595130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10518968	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17821190	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1850272	0.91[ASN][1000 genomes]
rs28430899	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28454770	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55819716	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56152791	0.87[ASN][1000 genomes]
rs56247511	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv833024	chr15:58447459-58621963	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv904266	chr15:58580921-58689187	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8024062	TROAP	trans	cerebellum	SCAN
rs8024062	RSL24D1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58587400-58598800	Weak transcription	Fetal Kidney	kidney
2	chr15:58590200-58602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:58592000-58595200	Weak transcription	Fetal Thymus	thymus
4	chr15:58592000-58598600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:58593400-58598400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:58594600-58595200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:58594600-58595400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:58594600-58595400	Enhancers	Liver	Liver
9	chr15:58594600-58595600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr15:58594800-58595600	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr15:58594800-58596000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr15:58595000-58595200	Weak transcription	Thymus	Thymus
13	chr15:58595000-58595800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr15:58595000-58598800	Weak transcription	Adipose Nuclei	Adipose
15	chr15:58595000-58598800	Weak transcription	Fetal Muscle Leg	muscle

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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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