Variant report

Variant	rs11858678
Chromosome Location	chr15:41467932-41467933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41221339..41222906-chr15:41467229..41469481,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10152855	0.85[ASN][1000 genomes]
rs11070321	0.93[ASN][1000 genomes]
rs11853192	0.84[EUR][1000 genomes]
rs11855102	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11855248	0.82[MEX][hapmap]
rs11855797	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11856848	0.86[MEX][hapmap]
rs11858115	0.92[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs12101934	0.81[EUR][1000 genomes]
rs12324159	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1659227	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678750	0.86[MEX][hapmap]
rs16971693	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs16971700	0.82[ASN][1000 genomes]
rs1717198	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1866400	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1965139	0.83[EUR][1000 genomes]
rs1965140	0.84[EUR][1000 genomes]
rs1971131	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1983400	0.84[EUR][1000 genomes]
rs2083239	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2164996	0.92[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2306083	0.82[MEX][hapmap]
rs2578655	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28409265	0.83[EUR][1000 genomes]
rs28409432	0.90[EUR][1000 genomes]
rs28493237	0.85[ASN][1000 genomes]
rs28495204	0.85[ASN][1000 genomes]
rs28510775	0.83[EUR][1000 genomes]
rs28516683	0.90[EUR][1000 genomes]
rs28568756	0.84[EUR][1000 genomes]
rs28613002	0.84[EUR][1000 genomes]
rs28665387	0.88[EUR][1000 genomes]
rs28688742	0.84[EUR][1000 genomes]
rs28735224	0.84[EUR][1000 genomes]
rs28828670	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2899013	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2918462	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2925345	0.82[MEX][hapmap]
rs2927061	0.86[MEX][hapmap]
rs2927062	0.86[MEX][hapmap]
rs2928141	0.98[ASN][1000 genomes]
rs2928156	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2947493	0.84[EUR][1000 genomes]
rs2947494	0.84[EUR][1000 genomes]
rs3100807	0.86[MEX][hapmap]
rs3101436	0.86[MEX][hapmap]
rs41442144	0.82[ASN][1000 genomes]
rs4258585	0.85[ASN][1000 genomes]
rs4419033	0.82[EUR][1000 genomes]
rs4445868	0.86[EUR][1000 genomes]
rs4592624	0.83[EUR][1000 genomes]
rs476633	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs494490	0.89[GIH][hapmap];0.87[TSI][hapmap]
rs537244	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551482	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55756301	0.86[ASN][1000 genomes]
rs56082289	0.86[ASN][1000 genomes]
rs561301	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56837771	0.94[ASN][1000 genomes]
rs57943533	0.93[ASN][1000 genomes]
rs58083671	0.89[ASN][1000 genomes]
rs58644012	0.98[ASN][1000 genomes]
rs59389433	0.86[ASN][1000 genomes]
rs59616518	0.89[ASN][1000 genomes]
rs59691280	0.86[ASN][1000 genomes]
rs60249025	0.89[ASN][1000 genomes]
rs60422198	0.89[ASN][1000 genomes]
rs61203391	0.81[EUR][1000 genomes]
rs61495227	0.88[ASN][1000 genomes]
rs61586152	0.94[ASN][1000 genomes]
rs6492983	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492988	0.94[ASN][1000 genomes]
rs6492991	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492992	0.81[ASN][1000 genomes]
rs6492993	0.84[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6492994	0.86[EUR][1000 genomes]
rs6492997	0.84[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs6492998	0.83[TSI][hapmap]
rs66471237	0.88[ASN][1000 genomes]
rs66510055	0.89[ASN][1000 genomes]
rs66602495	0.96[ASN][1000 genomes]
rs67531333	0.89[ASN][1000 genomes]
rs68133575	0.98[ASN][1000 genomes]
rs690733	1.00[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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs691672	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs691702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs692153	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs692195	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs692335	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7162443	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7162503	0.80[EUR][1000 genomes]
rs7165931	0.94[ASN][1000 genomes]
rs7166205	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7166905	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167813	0.83[EUR][1000 genomes]
rs7169375	0.82[MEX][hapmap]
rs7170049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7170913	0.89[ASN][1000 genomes]
rs7173086	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]
rs7173841	0.91[EUR][1000 genomes]
rs7175912	0.92[ASW][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs7178840	0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7179231	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7179676	0.93[ASN][1000 genomes]
rs7179969	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7180853	0.88[EUR][1000 genomes]
rs72737765	0.96[ASN][1000 genomes]
rs73396329	0.96[ASN][1000 genomes]
rs73396336	0.97[ASN][1000 genomes]
rs73396340	0.93[ASN][1000 genomes]
rs8023638	0.97[ASN][1000 genomes]
rs8026858	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8027932	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8029792	0.98[ASN][1000 genomes]
rs8032589	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs8033435	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8035252	0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs8037302	0.95[ASN][1000 genomes]
rs8038834	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8039014	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs8039915	0.86[ASN][1000 genomes]
rs8039934	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8043253	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs909023	0.94[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs909024	0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs909025	0.89[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9888710	0.90[EUR][1000 genomes]
rs9888718	0.92[EUR][1000 genomes]
rs9972345	0.94[ASN][1000 genomes]
rs9972349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9972622	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9972623	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv904109	chr15:41410705-41481254	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11858678	NDUFAF1	cis	cerebellum	SCAN
rs11858678	BUB1B	cis	parietal	SCAN
rs11858678	GPR176	cis	parietal	SCAN
rs11858678	NDUFAF1	cis	parietal	SCAN
rs11858678	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs11858678	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs11858678	NDUFAF1	cis	lymphoblastoid	seeQTL
rs11858678	BMF	cis	parietal	SCAN
rs11858678	CASC5	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41462600-41468000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr15:41467800-41468200	Active TSS	Monocytes-CD14+_RO01746	blood

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