Variant report

Variant	rs12662869
Chromosome Location	chr6:25784481-25784482
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25782886..25784532-chr6:25787589..25789523,2	MCF-7	breast:
2	chr6:25782991..25785483-chr6:25990675..25992482,2	MCF-7	breast:
3	chr6:25772361..25773981-chr6:25782511..25784752,2	K562	blood:

Variant related genes	Relation type
ENSG00000272065	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10946793	0.86[CEU][hapmap]
rs10946798	0.80[ASN][1000 genomes]
rs1141034	0.95[CEU][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1165151	0.85[JPT][hapmap]
rs1165153	0.85[JPT][hapmap]
rs1165155	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1165156	0.95[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1165157	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1165181	0.86[CEU][hapmap]
rs1165196	0.85[JPT][hapmap]
rs1165208	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1165209	0.85[JPT][hapmap]
rs1165211	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1165213	0.85[JPT][hapmap]
rs1165215	0.85[JPT][hapmap]
rs1165216	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1179086	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11794	0.86[CEU][hapmap]
rs1183200	0.85[JPT][hapmap]
rs1185567	0.85[JPT][hapmap]
rs1185976	0.91[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap]
rs12209856	0.95[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12663099	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs1317510	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1317816	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1318016	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13197601	0.85[JPT][hapmap]
rs1408271	0.91[CEU][hapmap]
rs1575535	0.95[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs17267614	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs1747522	0.81[JPT][hapmap]
rs1892245	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1892246	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1892248	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1937127	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1937129	0.87[EUR][1000 genomes]
rs2000350	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2000351	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2070642	0.91[CEU][hapmap];0.85[GIH][hapmap]
rs2096386	0.92[GIH][hapmap]
rs2154218	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2275904	0.80[AMR][1000 genomes]
rs2275905	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2762353	0.85[JPT][hapmap]
rs3757131	0.85[JPT][hapmap]
rs3778272	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3799352	0.85[JPT][hapmap]
rs3922681	0.88[CEU][hapmap]
rs3922699	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs3922842	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs3923	0.95[GIH][hapmap]
rs3923725	0.85[CEU][hapmap]
rs4131670	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs4132072	0.86[CEU][hapmap]
rs4360119	0.81[AMR][1000 genomes]
rs4360128	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs4464787	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs4711093	0.86[CEU][hapmap]
rs4711095	0.86[CEU][hapmap]
rs4711096	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs4711097	0.86[CEU][hapmap]
rs4712959	0.86[CEU][hapmap]
rs4712960	0.86[CEU][hapmap]
rs4712961	0.86[CEU][hapmap]
rs4712968	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4712970	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4712971	0.80[AMR][1000 genomes]
rs6456693	0.82[JPT][hapmap]
rs6456694	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs6924794	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs6926425	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937800	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7450798	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs7746502	0.93[JPT][hapmap]
rs7749149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7769908	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7770037	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9348692	0.86[CEU][hapmap]
rs9348694	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs9348695	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9348696	0.85[EUR][1000 genomes]
rs9356984	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs9356986	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs9356987	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs9356988	0.86[CEU][hapmap]
rs9358871	0.86[CEU][hapmap]
rs9358872	0.86[CEU][hapmap]
rs9358873	0.85[CEU][hapmap]
rs9358875	0.90[CEU][hapmap]
rs9358876	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs9358877	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs9358886	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs9358887	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9366627	0.91[CEU][hapmap]
rs9379778	0.86[CEU][hapmap]
rs9379783	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs9379784	0.86[CEU][hapmap]
rs9379785	0.86[CEU][hapmap]
rs9379786	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs9393659	0.81[CHB][hapmap]
rs9393661	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs9393662	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs9393670	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9393671	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12662869	SCGN	cis	cerebellum	SCAN
rs12662869	HIST1H3B	cis	cerebellum	SCAN
rs12662869	HIST1H1C	cis	parietal	SCAN
rs12662869	HIST1H2BF	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25773800-25788600	Weak transcription	Pancreas	Pancrea
2	chr6:25780400-25798800	Weak transcription	Liver	Liver
3	chr6:25781000-25786800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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