Variant report

Variant	rs2469409
Chromosome Location	chr8:3504575-3504576
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1384196	1.00[YRI][hapmap]
rs1905100	0.87[CEU][hapmap]
rs2449205	0.91[YRI][hapmap]
rs2469407	0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025209	chr8:3067655-3754882	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026998	chr8:3102679-3593264	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1034076	chr8:3168033-3989947	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv539351	chr8:3168033-3989947	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017164	chr8:3174168-4026811	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv539352	chr8:3174168-4026811	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1018218	chr8:3180287-4089011	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1028926	chr8:3318340-3667389	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv539353	chr8:3318340-3667389	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2469409	RPL23AP53	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:3503200-3504600	Enhancers	Brain Substantia Nigra	brain
2	chr8:3503200-3504800	Enhancers	Brain Cingulate Gyrus	brain
3	chr8:3504000-3504600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr8:3504000-3504600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr8:3504000-3504600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr8:3504000-3504600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr8:3504000-3504600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:3504000-3504800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr8:3504000-3505000	Enhancers	Fetal Lung	lung
10	chr8:3504200-3504600	Active TSS	Brain Anterior Caudate	brain
11	chr8:3504200-3504800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr8:3504400-3504800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr8:3504400-3504800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:3504400-3504800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr8:3504400-3504800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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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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