Variant report

Variant	rs390536
Chromosome Location	chr8:90869350-90869351
allele	C/T
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	chr8:90867270..90880457-chr8:90913050..90918593,18	MCF-7	breast:
2	chr8:90869160..90871090-chr8:90871381..90873801,2	MCF-7	breast:
3	chr8:90869094..90872518-chr8:90873810..90876034,4	MCF-7	breast:
4	chr8:90868769..90874649-chr8:90891359..90894975,5	MCF-7	breast:
5	chr8:90866711..90872793-chr8:90887380..90891820,9	MCF-7	breast:
6	chr8:90737773..90739680-chr8:90867503..90870182,2	MCF-7	breast:
7	chr8:90858582..90866507-chr8:90866541..90873248,10	MCF-7	breast:
8	chr8:90866902..90871267-chr8:90912071..90916231,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000207359	Chromatin interaction
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12675822	0.84[ASN][1000 genomes]
rs12679902	0.84[ASN][1000 genomes]
rs12680009	0.84[ASN][1000 genomes]
rs13277948	0.84[ASN][1000 genomes]
rs2189025	0.83[ASN][1000 genomes]
rs365871	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs366867	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs367640	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs370282	0.86[JPT][hapmap]
rs376962	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs379015	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380425	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs381456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386587	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386857	0.91[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs388866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398959	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs400571	0.91[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs40250	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs40459	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[ASN][1000 genomes]
rs40547	0.86[JPT][hapmap]
rs40638	0.86[JPT][hapmap]
rs410577	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs410663	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs418634	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs419890	0.93[ASN][1000 genomes]
rs42186	0.93[ASN][1000 genomes]
rs42346	0.86[JPT][hapmap]
rs42481	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs425140	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs427854	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs432457	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs447989	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs390536	OSGIN2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90861000-90870200	Weak transcription	HMEC	breast
2	chr8:90861000-90871000	Weak transcription	Right Atrium	heart
3	chr8:90861200-90869600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr8:90861200-90869800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr8:90861800-90870200	Weak transcription	Brain Hippocampus Middle	brain
6	chr8:90864800-90870400	Weak transcription	Aorta	Aorta
7	chr8:90866600-90873400	Enhancers	HSMMtube	muscle
8	chr8:90867000-90870400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr8:90867400-90869400	Enhancers	Primary B cells from peripheral blood	blood
10	chr8:90867600-90871200	Enhancers	Fetal Muscle Leg	muscle
11	chr8:90867800-90870200	Enhancers	A549	lung
12	chr8:90868200-90871200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr8:90868200-90872000	Enhancers	HSMM	muscle
14	chr8:90868400-90869600	Enhancers	Ovary	ovary
15	chr8:90868400-90870200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr8:90868600-90870200	Weak transcription	Colon Smooth Muscle	Colon
17	chr8:90868800-90869400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr8:90868800-90869600	Enhancers	Placenta	Placenta
19	chr8:90868800-90869800	Weak transcription	Brain Substantia Nigra	brain
20	chr8:90868800-90871200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:90869000-90869400	Enhancers	Fetal Muscle Trunk	muscle
22	chr8:90869000-90869600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr8:90869000-90872000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr8:90869200-90869800	Enhancers	Brain Anterior Caudate	brain
25	chr8:90869200-90870200	Weak transcription	Pancreas	Pancrea
26	chr8:90869200-90870400	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr8:90869200-90871200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr8:90869200-90873800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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