Variant report

Variant	rs2040071
Chromosome Location	chr9:15393381-15393382
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	chr9:15393231..15396045-chr9:15401354..15402871,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10122299	0.82[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs10962020	0.97[ASN][1000 genomes]
rs2382529	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2487860	0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs2488955	0.97[ASN][1000 genomes]
rs2488956	0.97[ASN][1000 genomes]
rs2488960	0.95[ASN][1000 genomes]
rs2488967	0.96[ASN][1000 genomes]
rs2488968	0.96[ASN][1000 genomes]
rs2490863	0.96[ASN][1000 genomes]
rs2798708	0.97[ASN][1000 genomes]
rs2798710	0.97[ASN][1000 genomes]
rs2798711	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798713	0.94[ASN][1000 genomes]
rs2798714	0.96[ASN][1000 genomes]
rs2798715	0.96[ASN][1000 genomes]
rs2798716	0.97[ASN][1000 genomes]
rs2798718	0.96[ASN][1000 genomes]
rs2798719	0.97[ASN][1000 genomes]
rs2798720	0.97[ASN][1000 genomes]
rs2798721	0.97[ASN][1000 genomes]
rs2798722	0.96[ASN][1000 genomes]
rs2798723	0.96[ASN][1000 genomes]
rs2798724	0.96[ASN][1000 genomes]
rs2798741	0.95[ASN][1000 genomes]
rs2798742	0.95[ASN][1000 genomes]
rs2798743	0.95[ASN][1000 genomes]
rs2804996	0.97[ASN][1000 genomes]
rs2804997	0.95[ASN][1000 genomes]
rs2805000	0.97[ASN][1000 genomes]
rs2805004	0.96[ASN][1000 genomes]
rs2805005	0.97[ASN][1000 genomes]
rs2805006	0.97[ASN][1000 genomes]
rs2805007	0.96[ASN][1000 genomes]
rs28870710	0.94[ASN][1000 genomes]
rs4741498	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs62573012	0.89[ASN][1000 genomes]
rs6474912	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1032861	chr9:15378192-15410429	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1022227	chr9:15379786-15416659	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2040071	C9orf150	cis	cerebellum	SCAN
rs2040071	PSIP1	cis	cerebellum	SCAN
rs2040071	DENND4C	cis	parietal	SCAN
rs2040071	CYP7B1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15387400-15393800	Enhancers	Fetal Intestine Large	intestine
2	chr9:15388400-15394200	Enhancers	Fetal Intestine Small	intestine
3	chr9:15391400-15400800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:15392200-15393400	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr9:15392600-15393400	Enhancers	Rectal Mucosa Donor 31	rectum

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