Variant report

Variant	rs6496979
Chromosome Location	chr15:93268739-93268740
allele	A/G
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	FOS	chr15:93268531-93268840	MCF10A-Er-Src	breast:	n/a	chr15:93268716-93268728
2	RAD21	chr15:93268223-93268833	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr15:93268085-93269109	ECC-1	luminal epithelium:	n/a	n/a
4	FOS	chr15:93268664-93268789	MCF10A-Er-Src	breast:	n/a	chr15:93268716-93268728
5	FOS	chr15:93268496-93268865	MCF10A-Er-Src	breast:	n/a	chr15:93268716-93268728
6	STAT3	chr15:93268485-93268885	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr15:93268222-93268914	ECC-1	luminal epithelium:	n/a	chr15:93268689-93268702
8	ESR1	chr15:93268149-93268892	ECC-1	luminal epithelium:	n/a	n/a
9	NR3C1	chr15:93268373-93268753	ECC-1	luminal epithelium:	n/a	n/a
10	ESR1	chr15:93268280-93268816	ECC-1	luminal epithelium:	n/a	n/a
11	FOXM1	chr15:93268052-93269140	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr15:93268241-93268906	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr15:93268087-93269012	ECC-1	luminal epithelium:	n/a	n/a
14	TCF12	chr15:93268079-93269049	ECC-1	luminal epithelium:	n/a	n/a
15	ESR1	chr15:93268158-93268965	ECC-1	luminal epithelium:	n/a	n/a
16	NFIC	chr15:93268081-93269012	ECC-1	luminal epithelium:	n/a	n/a
17	CEBPB	chr15:93268330-93268858	ECC-1	luminal epithelium:	n/a	chr15:93268689-93268702
18	EP300	chr15:93268124-93269032	ECC-1	luminal epithelium:	n/a	n/a
19	ESR1	chr15:93268315-93268789	ECC-1	luminal epithelium:	n/a	n/a
20	MYC	chr15:93268562-93268804	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr15:93268495-93268800	MCF10A-Er-Src	breast:	n/a	n/a
22	ESR1	chr15:93268231-93268845	ECC-1	luminal epithelium:	n/a	n/a
23	YY1	chr15:93268270-93268897	ECC-1	luminal epithelium:	n/a	n/a
24	TEAD4	chr15:93268120-93269078	ECC-1	luminal epithelium:	n/a	n/a
25	FOS	chr15:93268524-93268865	MCF10A-Er-Src	breast:	n/a	chr15:93268716-93268728
26	TEAD4	chr15:93268155-93269000	ECC-1	luminal epithelium:	n/a	n/a
27	FOXM1	chr15:93268055-93269148	ECC-1	luminal epithelium:	n/a	n/a
28	TCF12	chr15:93268133-93268936	ECC-1	luminal epithelium:	n/a	n/a
29	STAT3	chr15:93268461-93268806	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93267015..93268960-chr15:93276120..93278418,2	K562	blood:

Variant related genes	Relation type
ENSG00000272298	TF binding region
ENSG00000258741	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1004309	0.91[EUR][1000 genomes]
rs11854403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12440617	0.88[EUR][1000 genomes]
rs12441089	0.90[EUR][1000 genomes]
rs12442748	0.84[EUR][1000 genomes]
rs12899027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1808818	0.88[EUR][1000 genomes]
rs1971808	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2018744	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278519	0.90[EUR][1000 genomes]
rs2278520	0.90[EUR][1000 genomes]
rs2278521	0.90[EUR][1000 genomes]
rs2387911	0.91[EUR][1000 genomes]
rs2387913	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2387914	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2387915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34888918	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34981968	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35095971	0.86[EUR][1000 genomes]
rs35244027	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35257450	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35663415	0.88[EUR][1000 genomes]
rs35770033	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35982819	0.87[EUR][1000 genomes]
rs4777731	0.88[EUR][1000 genomes]
rs4777734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4778034	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57030748	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58112352	0.81[EUR][1000 genomes]
rs58407306	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59048995	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60471977	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6496972	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6496973	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6496974	1.00[CHB][hapmap];0.80[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6496975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6496976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6496977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6496978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6496982	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6496985	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66824972	0.89[EUR][1000 genomes]
rs66899661	0.89[EUR][1000 genomes]
rs67770259	0.88[EUR][1000 genomes]
rs67971141	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71462507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162983	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7163211	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7165223	0.85[EUR][1000 genomes]
rs7166307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7169147	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7169452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170586	0.81[ASN][1000 genomes]
rs7170733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7174515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7174670	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7176732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7176935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7177028	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183236	0.88[EUR][1000 genomes]
rs8025793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028966	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8029984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8032004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8033632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033698	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8039858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8041556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs893376	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9806135	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93258200-93277000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:93258200-93277000	Weak transcription	Left Ventricle	heart
3	chr15:93258400-93277000	Weak transcription	Ovary	ovary
4	chr15:93258600-93277000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:93258800-93277000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:93258800-93277000	Weak transcription	Fetal Brain Male	brain
7	chr15:93264400-93276600	Weak transcription	Fetal Kidney	kidney
8	chr15:93267600-93268800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr15:93267600-93277000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:93267600-93277000	Weak transcription	Right Ventricle	heart
11	chr15:93268200-93268800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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