Variant report

Variant	rs3729989
Chromosome Location	chr11:47370041-47370042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000134571	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11570058	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11570067	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11570072	0.89[AMR][1000 genomes]
rs11570078	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12285933	0.91[CEU][hapmap]
rs17726706	0.91[CEU][hapmap]
rs17726787	0.91[CEU][hapmap]
rs3736101	0.91[CEU][hapmap]
rs3816724	0.91[CEU][hapmap]
rs4647736	0.81[CEU][hapmap]
rs61897389	0.80[AMR][1000 genomes]
rs7102372	0.91[CEU][hapmap]
rs7112154	0.80[AMR][1000 genomes];0.85[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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3729989	ATG13	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47343200-47370600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr11:47351400-47375600	Weak transcription	Primary B cells from cord blood	blood
3	chr11:47353600-47375400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:47354800-47372800	Weak transcription	Gastric	stomach
5	chr11:47364000-47370600	Enhancers	Fetal Heart	heart
6	chr11:47364000-47372200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:47364600-47370600	Weak transcription	Spleen	Spleen
8	chr11:47367200-47372200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:47367800-47377200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:47368600-47374800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr11:47369000-47370200	Transcr. at gene 5' and 3'	Left Ventricle	heart
12	chr11:47369000-47371200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:47369200-47370200	Transcr. at gene 5' and 3'	Right Ventricle	heart
14	chr11:47369600-47372400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:47369800-47374400	Active TSS	Right Atrium	heart
16	chr11:47369800-47375600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr11:47370000-47374800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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

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