Variant report

Variant	rs7962366
Chromosome Location	chr12:12439062-12439063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12419697..12421689-chr12:12437095..12439954,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10431302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10431304	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772546	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772547	0.93[GIH][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs10845489	0.81[CEU][hapmap]
rs10845507	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11054754	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11609634	0.81[CEU][hapmap]
rs2284396	0.81[CEU][hapmap]
rs4477532	0.81[CEU][hapmap]
rs4763794	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4763795	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135274	0.80[EUR][1000 genomes]
rs7294695	0.81[CEU][hapmap]
rs7302808	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7956267	0.81[CHB][hapmap]
rs7965201	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7973531	0.93[GIH][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs7975772	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979787	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9300240	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
3	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7962366	LRP6	cis	parietal	SCAN
rs7962366	AICDA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12434400-12443000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:12436600-12446200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:12437000-12442200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:12437000-12447600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:12437600-12441200	Weak transcription	A549	lung
6	chr12:12437600-12443000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:12437600-12443800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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