Variant report

Variant	rs540375
Chromosome Location	chr5:152878727-152878728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs472792	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs498858	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518370	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524905	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542161	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548916	0.93[AMR][1000 genomes];0.97[EUR][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	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1019051	chr5:152550863-153057896	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv868912	chr5:152582002-153095306	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152872000-152886800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:152873400-152879400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:152873600-152884200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:152875200-152884000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:152876200-152879400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:152876200-152888400	Weak transcription	Brain Germinal Matrix	brain
7	chr5:152876800-152879400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:152876800-152896000	Weak transcription	Brain Anterior Caudate	brain
9	chr5:152877400-152878800	Weak transcription	Fetal Brain Male	brain
10	chr5:152877600-152884600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:152877800-152878800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:152878200-152879800	Weak transcription	Fetal Brain Female	brain
13	chr5:152878200-152880600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:152878200-152881400	Weak transcription	Aorta	Aorta
15	chr5:152878200-152884200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:152878600-152892400	Weak transcription	Muscle Satellite Cultured Cells	--

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dbSNP/dbVar ID: rs12345 /nsv7879
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