Variant report

Variant	rs470645
Chromosome Location	chr11:120007889-120007890
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2444240	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs470370	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs470373	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs470876	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs470941	0.88[JPT][hapmap]
rs471001	0.81[ASN][1000 genomes]
rs488672	1.00[JPT][hapmap]
rs4936509	0.92[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes]
rs533636	1.00[JPT][hapmap]
rs550164	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs561498	0.94[JPT][hapmap]
rs566935	0.94[JPT][hapmap]
rs573211	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs605374	0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs626225	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs670855	0.92[CEU][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs470645	DPAGT1	cis	cerebellum	SCAN
rs470645	UBE4A	cis	parietal	SCAN
rs470645	RNF214	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120000400-120008400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr11:120003200-120008200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:120005800-120008000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:120006000-120008800	Active TSS	Esophagus	oesophagus
5	chr11:120006200-120008800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:120006400-120008800	Active TSS	Placenta	Placenta
7	chr11:120006400-120008800	Active TSS	Fetal Thymus	thymus
8	chr11:120006400-120008800	Active TSS	Thymus	Thymus
9	chr11:120006600-120009000	Active TSS	HMEC	breast
10	chr11:120006600-120009200	Active TSS	NHEK	skin
11	chr11:120006800-120008600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:120006800-120009000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr11:120007000-120009000	Active TSS	Hela-S3	cervix
14	chr11:120007200-120021400	Weak transcription	Right Atrium	heart
15	chr11:120007800-120008800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:120007800-120010200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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