Variant report

Variant	rs56231040
Chromosome Location	chr14:104507049-104507050
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	chr14:104502438..104504952-chr14:104506998..104509553,2	MCF-7	breast:
2	chr14:104504865..104507694-chr14:104518320..104521249,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10136440	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10149651	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11160774	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11622475	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625697	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626404	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627297	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1187446	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1187448	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12878767	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12889168	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12895359	0.82[EUR][1000 genomes]
rs2005081	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273610	0.81[EUR][1000 genomes]
rs34288430	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34964872	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6576012	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7143682	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7143936	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8021692	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs941946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
4	nsv1049690	chr14:104411621-104575838	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv542208	chr14:104411621-104575838	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv526680	chr14:104427043-104568472	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1047990	chr14:104460605-104556463	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv542209	chr14:104497447-104540729	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1050479	chr14:104500427-104805738	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56231040	TDRD9	cis	Adipose Subcutaneous	GTEx
rs56231040	TDRD9	cis	lung	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104492200-104516000	Weak transcription	Spleen	Spleen
2	chr14:104496400-104520800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr14:104499000-104511800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr14:104502800-104513400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr14:104504600-104510400	Weak transcription	Gastric	stomach
6	chr14:104505800-104507200	Enhancers	Fetal Brain Male	brain
7	chr14:104506600-104507200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr14:104506600-104507200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:104506600-104507200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr14:104506800-104507200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr14:104506800-104507200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr14:104506800-104507400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr14:104506800-104510200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr14:104507000-104507200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:104507000-104507200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:104507000-104507200	Enhancers	Brain Anterior Caudate	brain

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