Variant report

Variant	rs12699560
Chromosome Location	chr7:13835262-13835263
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57922547..57924821-chr7:13833856..13835517,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10226447	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10234269	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10256467	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269432	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10269779	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10277842	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486070	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12699555	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12699556	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12699557	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12699558	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12699559	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024027	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051928	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2051929	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051930	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158802	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357753	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957915	0.89[ASN][1000 genomes]
rs766514	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs766515	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7783712	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786249	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7790528	0.82[EUR][1000 genomes]
rs7793540	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807547	0.82[EUR][1000 genomes]
rs9655108	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830909	chr7:13692329-13868294	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1019873	chr7:13707148-14133367	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv433032	chr7:13792450-13911001	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv887696	chr7:13801825-13857235	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv525915	chr7:13819302-13841798	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv519601	chr7:13819968-13857235	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv464388	chr7:13828099-13868913	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv606276	chr7:13828099-13868913	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12699560	TMEM106B	cis	parietal	SCAN
rs12699560	AGR3	cis	parietal	SCAN
rs12699560	NDUFA4	cis	parietal	SCAN
rs12699560	DGKB	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:13821800-13840400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:13833600-13836800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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