Variant report

Variant	rs3020075
Chromosome Location	chr11:93140986-93140987
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:93140894-93141393	K562	blood:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150
2	NFYA	chr11:93140809-93141025	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr11:93140968-93141348	K562	blood:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150
4	CEBPB	chr11:93140980-93141347	IMR90	lung:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150
5	FOS	chr11:93140976-93141333	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr11:93140897-93141476	HCT-116	colon:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150
7	EP300	chr11:93140926-93141303	K562	blood:	n/a	chr11:93141159-93141173 chr11:93141140-93141154
8	CEBPB	chr11:93140969-93141354	HepG2	liver:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150
9	CEBPB	chr11:93140982-93141344	A549	lung:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150
10	CEBPB	chr11:93140968-93141291	K562	blood:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150
11	CEBPB	chr11:93140958-93141353	Hela-S3	cervix:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150
12	FOS	chr11:93140982-93141346	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr11:93140976-93141342	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr11:93140940-93141345	HCT-116	colon:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150
15	JUND	chr11:93140982-93141348	K562	blood:	n/a	n/a
16	CEBPB	chr11:93140924-93141389	A549	lung:	n/a	chr11:93141160-93141177 chr11:93141162-93141173 chr11:93141136-93141153 chr11:93141139-93141150

Variant related genes	Relation type
CCDC67	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1004417	0.92[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1456239	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs1456242	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs1598546	0.85[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs1598547	0.88[EUR][1000 genomes]
rs1869913	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1960665	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1975819	0.87[EUR][1000 genomes]
rs2124559	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2259469	0.98[GIH][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2259630	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2260769	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605576	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2605577	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2605578	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2605579	0.98[GIH][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2658771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2658774	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2925353	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2925359	0.88[EUR][1000 genomes]
rs2925363	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3019203	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3019204	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3019218	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs3019219	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs3019220	0.87[EUR][1000 genomes]
rs3019227	0.88[EUR][1000 genomes]
rs3019229	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs3019230	0.92[EUR][1000 genomes]
rs3020055	0.83[EUR][1000 genomes]
rs3020070	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3020071	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3020072	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3020080	0.87[EUR][1000 genomes]
rs975916	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv1035530	chr11:93114111-93148948	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv555941	chr11:93129893-93181050	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv439	chr11:93135936-93171682	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv508649	chr11:93140899-93181092	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3020075	TYR	cis	cerebellum	SCAN
rs3020075	SNORA8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93126800-93145200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:93139000-93145200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:93140000-93144800	Weak transcription	Psoas Muscle	Psoas

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