Variant report

Variant	rs3858095
Chromosome Location	chr9:94904617-94904618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94903732..94905881-chr9:94913415..94915626,3	MCF-7	breast:
2	chr9:94901685..94904988-chr9:95003695..95006795,3	MCF-7	breast:
3	chr9:94902223..94905302-chr9:94908199..94910430,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196305	Chromatin interaction
ENSG00000225511	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10512220	0.87[CHB][hapmap]
rs10739925	0.87[CHB][hapmap]
rs10739926	0.88[ASN][1000 genomes]
rs10761143	0.87[CHB][hapmap]
rs10992251	0.96[CEU][hapmap]
rs1105085	0.99[ASN][1000 genomes]
rs11788534	0.82[ASN][1000 genomes]
rs11794148	0.89[ASN][1000 genomes]
rs12340044	0.87[CHB][hapmap]
rs1892268	0.87[CHB][hapmap]
rs1964170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2274921	0.94[ASW][hapmap];0.87[CEU][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs2297568	0.87[CHB][hapmap]
rs2895201	0.86[CHB][hapmap]
rs3847308	0.87[CHB][hapmap]
rs3927571	0.80[EUR][1000 genomes]
rs6479400	0.87[CHB][hapmap]
rs6479408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7020136	0.87[CHB][hapmap]
rs7023075	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs7024547	0.96[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7035786	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7041193	0.82[CHB][hapmap]
rs7042102	0.87[CHB][hapmap]
rs7848874	0.87[CHB][hapmap]
rs7866918	0.81[ASN][1000 genomes]
rs7869504	0.87[CHB][hapmap]
rs7871444	0.82[CHB][hapmap]
rs7873585	0.83[CHB][hapmap];0.91[JPT][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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv972778	chr9:94902068-94908273	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3858095	OMD	cis	cerebellum	SCAN
rs3858095	SPTLC1	cis	parietal	SCAN
rs3858095	ANKRD19	cis	parietal	SCAN
rs3858095	ZNF484	cis	parietal	SCAN
rs3858095	OMD	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94903000-94904800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr9:94903400-94904800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:94903400-94904800	Active TSS	HSMMtube	muscle
4	chr9:94903400-94905000	Active TSS	Osteobl	bone
5	chr9:94903400-94908800	Weak transcription	K562	blood
6	chr9:94903600-94904800	Active TSS	NHLF	lung
7	chr9:94903800-94906600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:94904000-94908800	Weak transcription	HMEC	breast
9	chr9:94904000-94909400	Weak transcription	Right Atrium	heart
10	chr9:94904200-94904800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:94904200-94904800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr9:94904200-94908200	Weak transcription	HUVEC	blood vessel
13	chr9:94904200-94908600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:94904200-94908600	Weak transcription	Ovary	ovary
15	chr9:94904200-94908800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr9:94904200-94909000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:94904200-94909000	Weak transcription	Gastric	stomach
18	chr9:94904400-94904800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:94904400-94908200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:94904400-94908400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:94904400-94908800	Weak transcription	NH-A	brain
22	chr9:94904600-94904800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:94904600-94905000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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