Variant report

Variant	rs7040762
Chromosome Location	chr9:118166766-118166767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10116195	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10124685	0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10817756	0.86[CEU][hapmap];0.94[JPT][hapmap]
rs10817758	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs10817774	0.86[EUR][1000 genomes]
rs10982719	0.89[JPT][hapmap]
rs10982722	0.83[ASN][1000 genomes]
rs10982724	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10982725	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10982726	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10982743	0.91[EUR][1000 genomes]
rs10982755	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10982757	0.89[EUR][1000 genomes]
rs10982762	0.84[EUR][1000 genomes]
rs10982764	0.90[EUR][1000 genomes]
rs11792811	0.86[EUR][1000 genomes]
rs11792823	0.86[EUR][1000 genomes]
rs11795062	0.86[EUR][1000 genomes]
rs12238100	0.86[EUR][1000 genomes]
rs2067094	0.91[EUR][1000 genomes]
rs34976516	0.81[EUR][1000 genomes]
rs3750505	0.93[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6478177	0.81[EUR][1000 genomes]
rs6478178	0.81[EUR][1000 genomes]
rs6478179	0.81[EUR][1000 genomes]
rs7018671	0.86[CEU][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs7029620	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7040283	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048279	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7848629	0.81[EUR][1000 genomes]
rs7853784	0.86[EUR][1000 genomes]
rs7854183	0.89[EUR][1000 genomes]
rs7860907	0.81[EUR][1000 genomes]
rs7864886	0.81[EUR][1000 genomes]
rs7868506	0.81[EUR][1000 genomes]
rs7869139	0.81[EUR][1000 genomes]
rs7871775	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9299225	0.81[EUR][1000 genomes]
rs9299228	0.81[EUR][1000 genomes]
rs9408863	0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9408864	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9408865	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9408866	0.81[EUR][1000 genomes]
rs9408867	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9408869	0.89[EUR][1000 genomes]
rs9408870	0.81[EUR][1000 genomes]
rs9409148	0.83[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9409149	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9409150	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9409154	0.82[EUR][1000 genomes]
rs9409155	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9409156	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9409159	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9409164	0.86[EUR][1000 genomes]
rs9409165	0.86[EUR][1000 genomes]
rs976734	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs981911	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919008	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1042957	chr9:118153824-118313540	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2761245	chr9:118157164-118171298	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7040762	C9orf29	cis	parietal	SCAN
rs7040762	ZNF618	cis	parietal	SCAN
rs7040762	DNAJC25	cis	parietal	SCAN
rs7040762	DEC1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118159000-118170600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:118160400-118173600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:118162200-118174000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr9:118164000-118169000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:118164200-118170000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:118164600-118169600	Weak transcription	NHDF-Ad	bronchial
7	chr9:118166000-118171600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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