Variant report

Variant	rs7173086
Chromosome Location	chr15:41509288-41509289
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41507375..41509488-chr15:41521656..41523869,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178997	Chromatin interaction
ENSG00000187446	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10152855	0.96[ASN][1000 genomes]
rs11070321	0.88[ASN][1000 genomes]
rs11070325	0.88[ASN][1000 genomes]
rs11070326	0.85[ASN][1000 genomes]
rs11855102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858115	1.00[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858678	0.92[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324159	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1659227	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16971693	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16971700	0.93[ASN][1000 genomes]
rs1717198	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1866400	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1965139	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1965140	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1971131	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs2083239	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2164996	1.00[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2578655	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28409265	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28493237	0.96[ASN][1000 genomes]
rs28495204	0.96[ASN][1000 genomes]
rs28568756	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28615543	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28665387	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28735224	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2899013	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2918462	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2928141	0.87[ASN][1000 genomes]
rs41442144	0.93[ASN][1000 genomes]
rs4258585	0.96[ASN][1000 genomes]
rs4419033	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4445868	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs494490	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs537244	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs551482	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55756301	0.97[ASN][1000 genomes]
rs56082289	0.97[ASN][1000 genomes]
rs56837771	0.89[ASN][1000 genomes]
rs57943533	0.88[ASN][1000 genomes]
rs58083671	0.92[ASN][1000 genomes]
rs58644012	0.86[ASN][1000 genomes]
rs59389433	0.97[ASN][1000 genomes]
rs59616518	0.93[ASN][1000 genomes]
rs59691280	0.97[ASN][1000 genomes]
rs60249025	0.93[ASN][1000 genomes]
rs60422198	0.93[ASN][1000 genomes]
rs61495227	0.91[ASN][1000 genomes]
rs61586152	0.85[ASN][1000 genomes]
rs6492988	0.89[ASN][1000 genomes]
rs6492991	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492992	0.92[ASN][1000 genomes]
rs6492993	0.92[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492994	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6492997	0.92[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6492998	0.81[TSI][hapmap]
rs66471237	0.91[ASN][1000 genomes]
rs66510055	0.90[ASN][1000 genomes]
rs66602495	0.85[ASN][1000 genomes]
rs67531333	0.90[ASN][1000 genomes]
rs68133575	0.86[ASN][1000 genomes]
rs690733	0.92[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs691702	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs692153	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs692335	0.83[ASN][1000 genomes]
rs7162443	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162503	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165931	0.89[ASN][1000 genomes]
rs7166205	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7166905	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7167813	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7170049	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7170913	0.93[ASN][1000 genomes]
rs7173841	0.80[EUR][1000 genomes]
rs7175912	1.00[ASW][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7178840	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7179231	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7179676	0.89[ASN][1000 genomes]
rs7179969	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs72737765	0.85[ASN][1000 genomes]
rs73396329	0.85[ASN][1000 genomes]
rs73396336	0.85[ASN][1000 genomes]
rs73396340	0.82[ASN][1000 genomes]
rs8023638	0.87[ASN][1000 genomes]
rs8026858	0.94[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs8029792	0.86[ASN][1000 genomes]
rs8032589	0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs8033435	0.81[EUR][1000 genomes]
rs8035252	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8036602	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8037302	0.84[ASN][1000 genomes]
rs8038834	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs8039014	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs8039915	0.97[ASN][1000 genomes]
rs8039934	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs8043253	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs909023	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs909024	0.88[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs909025	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9888718	0.80[EUR][1000 genomes]
rs9972345	0.89[ASN][1000 genomes]
rs9972349	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9972622	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9972623	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[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	nsv457120	chr15:41410705-41546631	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv569231	chr15:41410705-41546631	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1039906	chr15:41476209-41518976	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7173086	NDUFAF1	cis	lymphoblastoid	seeQTL
rs7173086	NUSAP1	cis	cerebellum	SCAN
rs7173086	NDUFAF1	cis	cerebellum	SCAN
rs7173086	BUB1B	cis	parietal	SCAN
rs7173086	BMF	cis	parietal	SCAN
rs7173086	NDUFAF1	cis	parietal	SCAN
rs7173086	NDUFAF1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41508800-41510600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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