Variant report

Variant	rs16829302
Chromosome Location	chr2:151885077-151885078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:151884261..151886924-chr2:151887279..151889141,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12464767	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12465152	0.80[EUR][1000 genomes]
rs12470183	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12470267	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12478652	0.93[EUR][1000 genomes]
rs1385418	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1476667	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1476668	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1476669	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1485132	0.92[JPT][hapmap]
rs16829166	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16829328	0.80[ASN][1000 genomes]
rs16829331	0.80[ASN][1000 genomes]
rs1962787	0.91[EUR][1000 genomes]
rs2086916	1.00[JPT][hapmap]
rs2220180	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2880193	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56748051	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58129209	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58558650	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58808803	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59864395	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62167197	0.80[ASN][1000 genomes]
rs62167199	0.80[ASN][1000 genomes]
rs62167200	0.80[ASN][1000 genomes]
rs6713372	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6730077	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6752241	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72997773	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7604218	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv525350	chr2:151711700-152044794	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1002140	chr2:151833257-152054910	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16829302	CACNB4	cis	parietal	SCAN
rs16829302	ARL5A	cis	parietal	SCAN
rs16829302	NEB	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151879200-151888400	Weak transcription	Fetal Stomach	stomach
2	chr2:151883800-151885200	Weak transcription	NHLF	lung
3	chr2:151883800-151886400	Enhancers	Fetal Lung	lung
4	chr2:151883800-151887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:151883800-151888800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:151884000-151885200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:151884000-151888800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:151884000-151889400	Weak transcription	Fetal Heart	heart
9	chr2:151884200-151885600	Weak transcription	Dnd41	blood
10	chr2:151884400-151885200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:151884800-151887200	Enhancers	NHDF-Ad	bronchial
12	chr2:151885000-151886200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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