Variant report

Variant	rs10406471
Chromosome Location	chr19:40658899-40658900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40650738..40653619-chr19:40655657..40658931,4	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10401980	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1327188	0.80[ASN][1000 genomes]
rs1327189	0.81[ASN][1000 genomes]
rs1327190	0.81[ASN][1000 genomes]
rs1327191	0.81[ASN][1000 genomes]
rs1327192	0.81[ASN][1000 genomes]
rs1327193	0.81[ASN][1000 genomes]
rs13344062	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16974093	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17797100	0.82[ASN][1000 genomes]
rs186815	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1998931	0.81[ASN][1000 genomes]
rs2569639	0.81[ASN][1000 genomes]
rs2569640	0.81[ASN][1000 genomes]
rs2569641	0.81[ASN][1000 genomes]
rs2569642	0.81[ASN][1000 genomes]
rs2569650	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2569651	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2767601	0.80[ASN][1000 genomes]
rs2767603	0.81[ASN][1000 genomes]
rs2819958	0.81[ASN][1000 genomes]
rs28629274	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28890790	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs337799	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs337800	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs337801	0.93[AMR][1000 genomes]
rs58003479	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73551642	0.81[ASN][1000 genomes]
rs73551661	0.82[ASN][1000 genomes]
rs73551662	0.82[ASN][1000 genomes]
rs73551663	0.82[ASN][1000 genomes]
rs73551668	0.82[ASN][1000 genomes]
rs73551674	0.82[ASN][1000 genomes]
rs73551675	0.82[ASN][1000 genomes]
rs73551681	0.82[ASN][1000 genomes]
rs73551683	0.81[ASN][1000 genomes]
rs73551685	0.82[ASN][1000 genomes]
rs73551687	0.82[ASN][1000 genomes]
rs73551688	0.82[ASN][1000 genomes]
rs73551689	0.82[ASN][1000 genomes]
rs73551691	0.82[ASN][1000 genomes]
rs73551695	0.83[ASN][1000 genomes]
rs73553603	0.95[ASN][1000 genomes]
rs8103294	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv911697	chr19:40599603-40711333	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv3336591	chr19:40647161-40670363	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10406471	AC005614.5	cis	lung	GTEx
rs10406471	ZNF780A	cis	lung	GTEx
rs10406471	ZNF780A	cis	Thyroid	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40654200-40673400	Weak transcription	Right Atrium	heart
2	chr19:40654400-40661000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:40655600-40660000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:40656600-40659000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr19:40656600-40661200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:40658200-40659600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:40658600-40659600	Enhancers	Primary hematopoietic stem cells	blood
8	chr19:40658600-40659600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:40658800-40659400	Enhancers	Monocytes-CD14+_RO01746	blood

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