Variant report

Variant	rs35209753
Chromosome Location	chr19:38389653-38389654
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38387761..38390868-chr19:38391934..38396797,4	MCF-7	breast:
2	chr19:38389120..38389982-chr19:38586169..38586708,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10401637	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10401968	0.83[EUR][1000 genomes]
rs10402530	0.84[EUR][1000 genomes]
rs10404567	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10409402	0.82[EUR][1000 genomes]
rs10409487	0.82[EUR][1000 genomes]
rs10420891	0.84[EUR][1000 genomes]
rs10427125	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11878269	0.83[EUR][1000 genomes]
rs11879180	0.84[EUR][1000 genomes]
rs12975057	0.84[EUR][1000 genomes]
rs1643462	0.83[EUR][1000 genomes]
rs1643463	0.83[EUR][1000 genomes]
rs1643466	0.83[EUR][1000 genomes]
rs1643467	0.83[EUR][1000 genomes]
rs1643468	0.83[EUR][1000 genomes]
rs1643469	0.86[EUR][1000 genomes]
rs1725477	0.83[EUR][1000 genomes]
rs1725478	0.83[EUR][1000 genomes]
rs1725480	0.83[EUR][1000 genomes]
rs1725481	0.83[EUR][1000 genomes]
rs1725482	0.83[EUR][1000 genomes]
rs1725483	0.83[EUR][1000 genomes]
rs1725485	0.83[EUR][1000 genomes]
rs1725487	0.83[EUR][1000 genomes]
rs1725488	0.81[EUR][1000 genomes]
rs1725494	0.85[EUR][1000 genomes]
rs2075281	0.83[EUR][1000 genomes]
rs2544718	0.85[EUR][1000 genomes]
rs353398	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs353399	0.87[EUR][1000 genomes]
rs353400	0.87[EUR][1000 genomes]
rs353402	0.87[EUR][1000 genomes]
rs353403	0.86[EUR][1000 genomes]
rs353404	0.87[EUR][1000 genomes]
rs353407	0.87[EUR][1000 genomes]
rs353414	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs353415	0.84[EUR][1000 genomes]
rs353416	0.87[EUR][1000 genomes]
rs353417	0.87[EUR][1000 genomes]
rs353419	0.87[EUR][1000 genomes]
rs353420	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs353421	0.87[EUR][1000 genomes]
rs353423	0.87[EUR][1000 genomes]
rs353424	0.87[EUR][1000 genomes]
rs353425	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs353426	0.86[EUR][1000 genomes]
rs353427	0.87[EUR][1000 genomes]
rs353428	0.83[EUR][1000 genomes]
rs353429	0.80[EUR][1000 genomes]
rs353430	0.85[EUR][1000 genomes]
rs3848626	0.82[EUR][1000 genomes]
rs4802135	0.86[EUR][1000 genomes]
rs4803509	0.83[EUR][1000 genomes]
rs4803524	0.84[EUR][1000 genomes]
rs58449039	0.83[EUR][1000 genomes]
rs705492	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs705494	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs705500	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7250409	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7250571	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7250868	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7252010	0.86[EUR][1000 genomes]
rs7257125	0.83[EUR][1000 genomes]
rs7258597	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs752878	0.83[EUR][1000 genomes]
rs8101752	0.82[EUR][1000 genomes]
rs8101858	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8102579	0.84[EUR][1000 genomes]
rs8104076	0.83[EUR][1000 genomes]
rs8107341	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8110284	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8182498	0.84[EUR][1000 genomes]
rs833895	0.80[EUR][1000 genomes]
rs833896	0.82[EUR][1000 genomes]
rs833897	0.83[EUR][1000 genomes]
rs833898	0.83[EUR][1000 genomes]
rs833926	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9304572	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35209753	WDR87	cis	Thyroid	GTEx
rs35209753	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38388200-38391200	Weak transcription	HSMMtube	muscle
2	chr19:38389200-38389800	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr19:38389200-38389800	Enhancers	Dnd41	blood
4	chr19:38389200-38389800	Enhancers	Hela-S3	cervix
5	chr19:38389200-38390000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38389200-38390000	Enhancers	A549	lung
7	chr19:38389200-38390200	Enhancers	Primary B cells from peripheral blood	blood
8	chr19:38389600-38389800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:38389600-38389800	Enhancers	Primary B cells from cord blood	blood
10	chr19:38389600-38389800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr19:38389600-38389800	Enhancers	Placenta	Placenta
12	chr19:38389600-38396600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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