Variant report

Variant	rs2024064
Chromosome Location	chr20:52612778-52612779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:52612633-52612864	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:56707941..56710505-chr20:52611192..52614067,2	MCF-7	breast:
2	chr17:56735310..56737024-chr20:52612265..52614955,3	MCF-7	breast:

Variant related genes	Relation type
BCAS1	TF binding region
ENSG00000212195	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1016279	0.87[CEU][hapmap];0.92[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10485440	0.83[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10485441	0.81[CEU][hapmap]
rs1125895	0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12480106	0.87[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477639	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024063	0.92[JPT][hapmap]
rs2024065	0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2108456	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276494	0.87[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276496	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276497	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276502	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276514	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2302039	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35575210	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3815270	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431061	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs55672258	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55776232	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6013861	0.95[ASN][1000 genomes]
rs6091793	0.81[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6091794	0.81[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6097716	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs714514	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7272317	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs8120953	0.92[JPT][hapmap]
rs8124068	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2024064	SLC9A8	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52601800-52630800	Weak transcription	Stomach Mucosa	stomach
3	chr20:52604400-52618200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52610800-52612800	Active TSS	HSMMtube	muscle
5	chr20:52612200-52614400	Enhancers	Brain Hippocampus Middle	brain
6	chr20:52612200-52614600	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr20:52612200-52614800	Enhancers	Brain Substantia Nigra	brain
8	chr20:52612400-52613400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr20:52612400-52613600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr20:52612400-52614400	Enhancers	Brain Anterior Caudate	brain
11	chr20:52612400-52614600	Enhancers	Brain Cingulate Gyrus	brain
12	chr20:52612600-52613000	Weak transcription	Brain Angular Gyrus	brain
13	chr20:52612600-52618600	Weak transcription	Rectal Mucosa Donor 31	rectum

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