Variant report

Variant	rs9428898
Chromosome Location	chr1:241982430-241982431
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:241972366..241975039-chr1:241979342..241982449,3	MCF-7	breast:
2	chr1:241980697..241983127-chr1:241987544..241989477,2	K562	blood:
3	chr1:241972003..241974042-chr1:241981060..241983771,2	K562	blood:
4	chr1:241980403..241982619-chr1:241984891..241986981,2	K562	blood:
5	chr1:241801162..241804735-chr1:241978255..241982638,4	K562	blood:
6	chr1:241964320..241966577-chr1:241982376..241983893,2	MCF-7	breast:
7	chr1:241975494..241979685-chr1:241981885..241985548,4	MCF-7	breast:
8	chr1:241797166..241800088-chr1:241982006..241983635,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000203668	Chromatin interaction
ENSG00000054277	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1017018	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10737868	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs10802990	0.81[JPT][hapmap]
rs10926564	0.83[JPT][hapmap]
rs10926569	0.86[CHD][hapmap];0.91[JPT][hapmap]
rs12022825	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12038477	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12042255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1418764	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1891566	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4129118	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs4658661	0.86[JPT][hapmap]
rs55865277	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59836392	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6413961	0.85[JPT][hapmap]
rs6429301	0.81[JPT][hapmap]
rs6666953	0.91[JPT][hapmap]
rs6669036	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs6669629	0.95[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs6680142	0.81[JPT][hapmap]
rs6695661	0.81[JPT][hapmap]
rs6696527	0.95[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap]
rs72755248	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72755251	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7418198	0.95[CEU][hapmap];0.91[JPT][hapmap]
rs7418599	0.81[JPT][hapmap]
rs7418764	0.95[CEU][hapmap];0.91[JPT][hapmap]
rs7530797	0.95[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap]
rs7551270	0.95[CEU][hapmap];0.91[JPT][hapmap]
rs9428515	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9428516	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9428520	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9428521	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9428524	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9428525	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9428527	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9428529	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9428891	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9428892	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9428893	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9428894	0.82[ASW][hapmap];0.85[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes]
rs9428899	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9428900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9428901	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9428902	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs952084	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv528015	chr1:241865219-242070731	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv2762521	chr1:241891040-242074222	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv873373	chr1:241939069-242027500	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv873374	chr1:241975147-242097624	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9428898	OPN3	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241981200-241984800	Weak transcription	A549	lung
2	chr1:241981200-241992000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:241981800-241984200	Weak transcription	Hela-S3	cervix
4	chr1:241981800-241984400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:241981800-241985200	Weak transcription	NHLF	lung
6	chr1:241981800-241989000	Weak transcription	Aorta	Aorta
7	chr1:241982000-241984200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:241982000-241984400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:241982200-241984000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:241982200-241984200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:241982200-241987000	Weak transcription	K562	blood

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