Variant report

Variant	rs28438984
Chromosome Location	chr15:44232086-44232087
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1008183	0.91[EUR][1000 genomes]
rs11070413	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070415	1.00[EUR][1000 genomes]
rs11070416	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11630936	0.97[EUR][1000 genomes]
rs11631901	0.94[EUR][1000 genomes]
rs11635039	0.94[EUR][1000 genomes]
rs11637468	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12439442	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440402	0.94[EUR][1000 genomes]
rs12442168	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16944774	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16945686	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16950215	0.97[EUR][1000 genomes]
rs2306674	0.94[EUR][1000 genomes]
rs28377221	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28542819	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28599486	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28685813	0.92[EUR][1000 genomes]
rs28706414	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3742981	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850777	0.97[EUR][1000 genomes]
rs530074	0.99[ASN][1000 genomes]
rs55927923	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60484809	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178452	0.97[EUR][1000 genomes]
rs9806129	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9920164	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription 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 miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28438984	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs28438984	ADAL	cis	Nerve Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44225400-44246200	Weak transcription	Right Atrium	heart
2	chr15:44225600-44246200	Weak transcription	NH-A	brain
3	chr15:44227200-44233400	Weak transcription	Brain Angular Gyrus	brain
4	chr15:44227200-44251000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:44227400-44234200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:44227400-44235800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:44227400-44244200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:44227600-44233400	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:44228400-44234000	Weak transcription	Brain Anterior Caudate	brain
10	chr15:44228400-44234400	Weak transcription	Brain Substantia Nigra	brain
11	chr15:44229000-44234400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:44229000-44245000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:44231000-44234400	Weak transcription	NHDF-Ad	bronchial
14	chr15:44232000-44232400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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