Variant report

Variant	rs6479387
Chromosome Location	chr9:94695011-94695012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94537471..94538153-chr9:94694764..94695511,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10116249	0.93[EUR][1000 genomes]
rs10118072	0.82[EUR][1000 genomes]
rs10118792	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10124760	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10125384	0.83[EUR][1000 genomes]
rs10125466	0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10512220	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10733743	0.87[EUR][1000 genomes]
rs10761135	0.86[JPT][hapmap]
rs10761137	0.84[CEU][hapmap]
rs10761138	0.93[EUR][1000 genomes]
rs10761143	0.80[CEU][hapmap]
rs10820918	0.99[ASN][1000 genomes]
rs10820931	0.87[EUR][1000 genomes]
rs11795130	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12340044	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs12685595	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1316268	0.92[EUR][1000 genomes]
rs1528363	0.83[JPT][hapmap]
rs1528364	0.83[JPT][hapmap]
rs1534533	0.83[JPT][hapmap]
rs1609292	0.84[CEU][hapmap]
rs1881389	0.83[ASW][hapmap]
rs1881391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892268	0.84[CEU][hapmap];0.88[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1919100	0.85[EUR][1000 genomes]
rs2297568	0.91[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2312739	0.85[EUR][1000 genomes]
rs2895201	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs3847308	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs4744111	0.83[JPT][hapmap]
rs4744112	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6479385	0.87[EUR][1000 genomes]
rs6479386	0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs6479388	0.92[EUR][1000 genomes]
rs6479389	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs6479400	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs6479402	0.82[EUR][1000 genomes]
rs7020136	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs7034357	0.92[EUR][1000 genomes]
rs7034363	0.88[EUR][1000 genomes]
rs7037255	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs7038017	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7041193	0.91[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs7042102	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs7047326	0.95[EUR][1000 genomes]
rs7048699	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs7848874	0.88[ASW][hapmap];0.88[CEU][hapmap]
rs7848987	0.83[EUR][1000 genomes]
rs7852032	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7853136	0.99[ASN][1000 genomes]
rs7858435	0.95[JPT][hapmap]
rs7859689	0.82[EUR][1000 genomes]
rs7862779	0.83[EUR][1000 genomes]
rs7863167	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7867072	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs7869504	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs7871444	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs9774945	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6479387	LOC100128076	cis	lymphoblastoid	seeQTL
rs6479387	ZNF484	cis	parietal	SCAN
rs6479387	CDK20	cis	parietal	SCAN
rs6479387	SPTLC1	cis	parietal	SCAN
rs6479387	ZNF484	cis	cerebellum	SCAN
rs6479387	C9orf170	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94686600-94696000	Weak transcription	Ovary	ovary
2	chr9:94690800-94696200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:94691000-94695400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:94693000-94695400	Weak transcription	Fetal Stomach	stomach
5	chr9:94693200-94697400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:94693400-94697200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:94694600-94697200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:94695000-94696200	Enhancers	Colon Smooth Muscle	Colon

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