Variant report

Variant	rs9869458
Chromosome Location	chr3:46038575-46038576
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	chr3:46038559-46038709	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46038061..46039576-chr3:46044215..46045732,2	K562	blood:

Variant related genes	Relation type
FYCO1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1392293	0.85[EUR][1000 genomes]
rs2036293	0.88[EUR][1000 genomes]
rs2101446	0.83[EUR][1000 genomes]
rs2133666	0.86[EUR][1000 genomes]
rs2371	0.92[EUR][1000 genomes]
rs2373148	0.92[EUR][1000 genomes]
rs2888511	0.92[EUR][1000 genomes]
rs4321566	0.88[EUR][1000 genomes]
rs4490404	0.86[EUR][1000 genomes]
rs4493468	0.86[EUR][1000 genomes]
rs4682801	0.83[EUR][1000 genomes]
rs4683158	0.86[EUR][1000 genomes]
rs4683171	0.88[EUR][1000 genomes]
rs6441938	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441939	0.92[EUR][1000 genomes]
rs6786959	0.86[EUR][1000 genomes]
rs6802312	0.83[EUR][1000 genomes]
rs6809223	0.95[EUR][1000 genomes]
rs7610953	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622333	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625348	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638309	0.92[EUR][1000 genomes]
rs7653682	0.83[EUR][1000 genomes]
rs904634	0.85[EUR][1000 genomes]
rs974380	0.92[EUR][1000 genomes]
rs974381	0.92[EUR][1000 genomes]
rs9811555	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46037600-46038800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:46037600-46053000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:46037600-46064600	Weak transcription	Gastric	stomach
4	chr3:46037800-46038800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:46037800-46039000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:46038000-46041800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:46038200-46038800	Enhancers	Dnd41	blood
8	chr3:46038200-46038800	Enhancers	GM12878-XiMat	blood
9	chr3:46038200-46038800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr3:46038200-46040200	Weak transcription	Fetal Thymus	thymus
11	chr3:46038200-46041800	Weak transcription	Brain Anterior Caudate	brain
12	chr3:46038200-46041800	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:46038200-46041800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:46038200-46042200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:46038200-46047400	Weak transcription	Psoas Muscle	Psoas

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