Variant report

Variant	rs12346966
Chromosome Location	chr9:73899875-73899876
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	chr9:73898945..73901446-chr9:74374124..74376228,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10081739	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10429473	0.90[ASN][1000 genomes]
rs10429502	0.90[ASN][1000 genomes]
rs10512008	0.85[ASN][1000 genomes]
rs10746866	0.83[ASN][1000 genomes]
rs10746870	0.83[ASN][1000 genomes]
rs10780998	0.80[ASN][1000 genomes]
rs10781000	0.83[ASN][1000 genomes]
rs10781003	0.83[ASN][1000 genomes]
rs10781007	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10781008	0.86[ASN][1000 genomes]
rs10781009	0.86[ASN][1000 genomes]
rs10868992	0.83[ASN][1000 genomes]
rs10868996	0.83[ASN][1000 genomes]
rs10868998	0.83[ASN][1000 genomes]
rs10869007	0.85[ASN][1000 genomes]
rs10869008	0.86[ASN][1000 genomes]
rs10869009	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11142746	0.80[ASN][1000 genomes]
rs11142748	0.83[ASN][1000 genomes]
rs11142756	0.83[ASN][1000 genomes]
rs11142767	0.86[ASN][1000 genomes]
rs11142768	0.86[ASN][1000 genomes]
rs11142770	0.87[ASN][1000 genomes]
rs11142775	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11142776	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11790079	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12337266	0.81[ASN][1000 genomes]
rs12338261	0.85[ASN][1000 genomes]
rs12351136	0.86[ASN][1000 genomes]
rs13287797	0.83[ASN][1000 genomes]
rs1354459	0.83[ASN][1000 genomes]
rs1504387	0.96[ASN][1000 genomes]
rs1580911	0.83[ASN][1000 genomes]
rs1604854	0.80[ASN][1000 genomes]
rs17056652	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2062863	0.90[ASN][1000 genomes]
rs2062864	0.90[ASN][1000 genomes]
rs2309908	0.83[ASN][1000 genomes]
rs2860097	0.86[ASN][1000 genomes]
rs4745075	0.80[ASN][1000 genomes]
rs62543438	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6560191	0.80[ASN][1000 genomes]
rs6560192	0.83[ASN][1000 genomes]
rs6560193	0.90[ASN][1000 genomes]
rs6560194	0.90[ASN][1000 genomes]
rs7022575	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7024365	0.83[ASN][1000 genomes]
rs7024634	0.83[ASN][1000 genomes]
rs7034708	0.83[ASN][1000 genomes]
rs7035975	0.82[ASN][1000 genomes]
rs7037178	0.90[ASN][1000 genomes]
rs7044209	0.90[ASN][1000 genomes]
rs719858	0.85[ASN][1000 genomes]
rs7850256	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7852254	0.82[ASN][1000 genomes]
rs7861071	0.80[ASN][1000 genomes]
rs7863093	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][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	nsv1035505	chr9:73709852-73934353	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv893442	chr9:73778502-74115344	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv893443	chr9:73859086-74008905	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv916062	chr9:73861614-74246247	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv614605	chr9:73887092-73915883	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12346966	DDX59	trans	cerebellum	SCAN
rs12346966	FAM108B1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73887200-73900200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:73895200-73900200	Weak transcription	Liver	Liver
3	chr9:73896400-73900400	Weak transcription	HepG2	liver

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