Variant report

Variant	rs2323729
Chromosome Location	chr13:38639677-38639678
allele	C/T
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	FOXA2	chr13:38639649-38640295	A549	lung:	n/a	n/a
2	POLR2A	chr13:38639580-38639694	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
LINC00571	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1073835	0.81[EUR][1000 genomes]
rs12050067	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1360921	0.81[EUR][1000 genomes]
rs1360922	0.83[EUR][1000 genomes]
rs1360923	0.81[EUR][1000 genomes]
rs4262828	0.81[EUR][1000 genomes]
rs4539457	0.81[EUR][1000 genomes]
rs4941883	0.81[EUR][1000 genomes]
rs4943560	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56320674	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61956980	0.81[EUR][1000 genomes]
rs7334221	0.82[EUR][1000 genomes]
rs7336735	0.82[EUR][1000 genomes]
rs7988853	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7994611	0.81[EUR][1000 genomes]
rs9315543	0.81[EUR][1000 genomes]
rs9532159	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9532160	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9548172	0.82[EUR][1000 genomes]
rs9548179	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9566296	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9566299	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9566300	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9576428	0.81[EUR][1000 genomes]
rs9576429	0.81[EUR][1000 genomes]
rs9576445	0.88[AMR][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	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv900000	chr13:38608928-38710260	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv900001	chr13:38619750-38710260	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv900002	chr13:38628041-38710260	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv274978	chr13:38633467-38659853	Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv3400710	chr13:38639001-38670017	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2323729	LINC00571	cis	Thyroid	GTEx
rs2323729	LINC00571	cis	Esophagus Muscularis	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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