Variant report

Variant	rs2441872
Chromosome Location	chr8:105175796-105175797
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:105173950..105176285-chr8:105193428..105195940,2	MCF-7	breast:
2	chr8:105153535..105155055-chr8:105174946..105177136,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10955342	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11776859	0.88[EUR][1000 genomes]
rs12674899	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13261882	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13270385	0.85[EUR][1000 genomes]
rs13270802	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1545370	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1816933	0.89[EUR][1000 genomes]
rs1816934	0.91[EUR][1000 genomes]
rs2044534	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2441874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2441875	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2441877	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2441878	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2441879	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2441882	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2441884	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2511637	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2511638	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34974046	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35376345	0.91[AMR][1000 genomes];0.95[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	nsv1031195	chr8:104601231-105194208	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	esv1847227	chr8:105025912-105251147	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv891251	chr8:105054446-105283340	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv891252	chr8:105106882-105227985	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv831416	chr8:105137789-105296965	Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2441872	SPAG1	cis	parietal	SCAN
rs2441872	LRP12	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105156400-105188400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:105174200-105177000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr8:105174400-105179200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr8:105175200-105176400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr8:105175400-105176600	Enhancers	Primary neutrophils fromperipheralblood	blood

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