Variant report

Variant	rs9790169
Chromosome Location	chr3:134151959-134151960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13074557	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13088645	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13097818	0.83[AMR][1000 genomes]
rs1366067	0.88[CHB][hapmap]
rs1391695	0.89[CHB][hapmap]
rs3846053	0.82[AMR][1000 genomes]
rs3846054	0.82[AMR][1000 genomes]
rs4602357	0.82[AMR][1000 genomes]
rs6767595	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7611834	1.00[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7628967	0.82[AMR][1000 genomes]
rs7647128	0.83[AMR][1000 genomes]
rs7650509	0.89[CHB][hapmap]
rs9847750	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv877510	chr3:134126150-134400448	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1007607	chr3:134131521-134156814	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9790169	ANAPC13	cis	Nerve Tibial	GTEx
rs9790169	ANAPC13	cis	Muscle Skeletal	GTEx
rs9790169	ANAPC13	cis	Artery Tibial	GTEx
rs9790169	CEP63	cis	Nerve Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134148000-134156000	Weak transcription	NHEK	skin
2	chr3:134148400-134159200	Weak transcription	Osteobl	bone
3	chr3:134149600-134154200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:134150200-134152400	Weak transcription	A549	lung
5	chr3:134150400-134155800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:134151200-134152000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:134151400-134154800	Weak transcription	Right Atrium	heart

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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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