Variant report

Variant	rs605374
Chromosome Location	chr11:120005633-120005634
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1790476	0.97[EUR][1000 genomes]
rs2444240	0.87[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs470370	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs470373	0.85[ASN][1000 genomes]
rs470411	1.00[CEU][hapmap];0.92[YRI][hapmap];0.96[EUR][1000 genomes]
rs470645	0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs470725	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs470876	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs470941	0.87[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs471001	0.82[ASN][1000 genomes]
rs488672	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs531260	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs533636	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs550164	0.86[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs561498	0.86[CEU][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs566935	0.94[JPT][hapmap]
rs573211	0.81[ASN][1000 genomes]
rs670855	0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs896691	0.82[EUR][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs605374	TRIM29	cis	Artery Tibial	GTEx
rs605374	THY1	cis	cerebellum	SCAN
rs605374	SORL1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119999000-120006400	Enhancers	Placenta	Placenta
2	chr11:120000400-120008400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:120000600-120006400	Weak transcription	Fetal Thymus	thymus
4	chr11:120001400-120007800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:120002000-120006000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:120002800-120006200	Transcr. at gene 5' and 3'	NHEK	skin
7	chr11:120003200-120008200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:120004000-120005800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:120004400-120005800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:120004400-120006000	Transcr. at gene 5' and 3'	Esophagus	oesophagus
11	chr11:120005200-120006600	Flanking Active TSS	HMEC	breast
12	chr11:120005600-120006000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr11:120005600-120007000	Flanking Active TSS	Hela-S3	cervix

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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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