Variant report

Variant	rs303525
Chromosome Location	chr10:90570304-90570305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:90341886..90344388-chr10:90569050..90571986,2	MCF-7	breast:
2	chr10:90487910..90488745-chr10:90570207..90570902,2	MCF-7	breast:
3	chr10:90324503..90325089-chr10:90570142..90570781,3	MCF-7	breast:
4	chr10:90447415..90448216-chr10:90569895..90570657,2	MCF-7	breast:
5	chr10:89576342..89578923-chr10:90569116..90571697,2	K562	blood:
6	chr10:90324669..90325526-chr10:90569662..90570692,3	MCF-7	breast:
7	chr10:90447351..90448271-chr10:90569724..90570693,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223820	Chromatin interaction
ENSG00000184719	Chromatin interaction
ENSG00000138138	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10749596	1.00[MKK][hapmap]
rs11202898	1.00[CHD][hapmap]
rs11202902	1.00[CHD][hapmap]
rs12254856	1.00[CHD][hapmap]
rs1411780	0.91[CEU][hapmap];1.00[CHD][hapmap]
rs1653842	1.00[CHD][hapmap]
rs1769692	1.00[CHD][hapmap]
rs2439707	1.00[CHD][hapmap]
rs2604962	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs303526	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs303527	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs376036	1.00[CHD][hapmap]
rs378308	1.00[CHD][hapmap]
rs390436	1.00[CHD][hapmap]
rs407433	1.00[CHD][hapmap]
rs434401	1.00[CHD][hapmap]
rs442545	1.00[CHD][hapmap]
rs451949	1.00[CHD][hapmap]
rs454439	1.00[CHD][hapmap]

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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv831941	chr10:90410488-90587332	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv1043015	chr10:90467067-90593692	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv467415	chr10:90478483-90600865	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv551840	chr10:90478483-90600865	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs303525	OPN4	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90569200-90570800	Enhancers	Fetal Thymus	thymus
2	chr10:90569400-90570600	Enhancers	Thymus	Thymus
3	chr10:90569600-90570600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr10:90569600-90570800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:90569600-90571000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:90569600-90571000	Enhancers	Hela-S3	cervix
7	chr10:90569600-90571200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr10:90569600-90571200	Enhancers	NHEK	skin
9	chr10:90569800-90570400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr10:90569800-90570400	Enhancers	A549	lung
11	chr10:90569800-90570600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr10:90569800-90570600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:90569800-90570600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr10:90569800-90571200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:90570000-90570400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr10:90570000-90570600	Enhancers	Primary T cells from cord blood	blood
17	chr10:90570000-90570600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:90570000-90570600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr10:90570000-90571000	Enhancers	HMEC	breast
20	chr10:90570000-90571000	Enhancers	NHLF	lung

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