Variant report

Variant	rs1560166
Chromosome Location	chr5:54170696-54170697
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	GATA3	chr5:54170162-54170821	MCF-7	breast:	n/a	n/a
2	CEBPB	chr5:54170301-54170907	MCF-7	breast:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
3	STAT3	chr5:54170098-54170764	Hela-S3	cervix:	n/a	chr5:54170641-54170649
4	NFIC	chr5:54170024-54170870	ECC-1	luminal epithelium:	n/a	n/a
5	FOS	chr5:54170239-54170727	MCF10A-Er-Src	breast:	n/a	chr5:54170619-54170631 chr5:54170305-54170315 chr5:54170305-54170315
6	FOS	chr5:54170200-54170810	MCF10A-Er-Src	breast:	n/a	chr5:54170619-54170631 chr5:54170305-54170315 chr5:54170305-54170315
7	TCF7L2	chr5:54170073-54170698	Hela-S3	cervix:	n/a	n/a
8	HDAC2	chr5:54170375-54170751	MCF-7	breast:	n/a	chr5:54170417-54170431
9	EP300	chr5:54170149-54170891	T-47D	breast:	n/a	n/a
10	EP300	chr5:54170012-54170769	ECC-1	luminal epithelium:	n/a	n/a
11	FOXM1	chr5:54170005-54170708	ECC-1	luminal epithelium:	n/a	n/a
12	ZKSCAN1	chr5:54170389-54171119	Hela-S3	cervix:	n/a	n/a
13	FOS	chr5:54170233-54170786	MCF10A-Er-Src	breast:	n/a	chr5:54170619-54170631 chr5:54170305-54170315 chr5:54170305-54170315
14	GATA3	chr5:54170276-54170847	T-47D	breast:	n/a	n/a
15	TFAP2C	chr5:54170251-54170702	Hela-S3	cervix:	n/a	n/a
16	SPI1	chr5:54170414-54170970	HL-60	blood:	n/a	n/a
17	CEBPB	chr5:54170541-54170776	A549	lung:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
18	CEBPB	chr5:54170512-54170782	HepG2	liver:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
19	MAX	chr5:54170247-54170796	Hela-S3	cervix:	n/a	n/a
20	GATA3	chr5:54170103-54170883	MCF-7	breast:	n/a	n/a
21	GATA3	chr5:54170214-54170870	T-47D	breast:	n/a	n/a
22	CEBPB	chr5:54170523-54170714	K562	blood:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
23	CEBPB	chr5:54170484-54170830	K562	blood:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
24	POLR2A	chr5:54170055-54170839	SK-N-MC	brain:	n/a	n/a
25	MYC	chr5:54170496-54170807	NB4	blood:	n/a	n/a
26	SPI1	chr5:54170562-54170864	HL-60	blood:	n/a	n/a
27	STAT3	chr5:54170252-54170737	MCF10A-Er-Src	breast:	n/a	chr5:54170641-54170649
28	MYC	chr5:54170321-54170798	MCF10A-Er-Src	breast:	n/a	n/a
29	KAP1	chr5:54170303-54170697	HEK293	kidney:	n/a	n/a
30	EP300	chr5:54170170-54170808	Hela-S3	cervix:	n/a	n/a
31	MYC	chr5:54170332-54170857	MCF10A-Er-Src	breast:	n/a	n/a
32	NFIC	chr5:54170089-54170736	ECC-1	luminal epithelium:	n/a	n/a
33	MAX	chr5:54170415-54170821	NB4	blood:	n/a	n/a
34	STAT3	chr5:54170559-54170814	MCF10A-Er-Src	breast:	n/a	chr5:54170641-54170649
35	CEBPB	chr5:54170171-54170837	ECC-1	luminal epithelium:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
36	TCF12	chr5:54170100-54170715	ECC-1	luminal epithelium:	n/a	n/a
37	BRCA1	chr5:54170238-54170757	Hela-S3	cervix:	n/a	n/a
38	CEBPB	chr5:54170137-54170859	Hela-S3	cervix:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
39	STAT3	chr5:54170127-54170727	MCF10A-Er-Src	breast:	n/a	chr5:54170641-54170649
40	CEBPB	chr5:54170325-54170939	MCF-7	breast:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
41	TFAP2A	chr5:54170232-54170733	Hela-S3	cervix:	n/a	chr5:54170405-54170420
42	CEBPB	chr5:54170458-54170815	ECC-1	luminal epithelium:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
43	TCF7L2	chr5:54170009-54170825	Hela-S3	cervix:	n/a	n/a
44	CEBPB	chr5:54170459-54170822	IMR90	lung:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651

Variant related genes	Relation type
ENSG00000232517	TF binding region
ENSG00000249843	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10040872	0.93[ASN][1000 genomes]
rs10042734	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1005622	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10056452	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10058862	0.80[EUR][1000 genomes]
rs10805469	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10805470	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10940430	0.98[ASN][1000 genomes]
rs10940431	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940432	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940434	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11738151	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11742711	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11953607	0.98[ASN][1000 genomes]
rs12515327	0.84[EUR][1000 genomes]
rs12657845	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13181749	0.99[ASN][1000 genomes]
rs1560165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17588816	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1965716	0.87[EUR][1000 genomes]
rs2017082	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2019005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564901	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2897758	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3916738	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3935813	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4242047	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4242050	0.94[ASN][1000 genomes]
rs4320216	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4446420	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4502767	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4865879	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865880	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865881	0.99[ASN][1000 genomes]
rs4865882	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6863705	0.82[CEU][hapmap]
rs734097	0.85[EUR][1000 genomes]
rs737526	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7709516	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs976645	0.81[AMR][1000 genomes];0.88[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	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv598179	chr5:54156269-54192823	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54168400-54171800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:54168600-54175600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:54169000-54171000	Enhancers	HUVEC	blood vessel
4	chr5:54169400-54171000	Enhancers	Osteobl	bone
5	chr5:54169400-54171400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:54169400-54171800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:54169600-54171000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:54169600-54171000	Enhancers	Adipose Nuclei	Adipose
9	chr5:54169600-54171400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr5:54169600-54171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:54169600-54171400	Enhancers	Hela-S3	cervix
12	chr5:54169800-54170800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:54169800-54171000	Enhancers	Liver	Liver
14	chr5:54169800-54171200	Weak transcription	Left Ventricle	heart
15	chr5:54170000-54171200	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr5:54170000-54171400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr5:54170000-54171400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr5:54170000-54171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:54170000-54178800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:54170200-54170800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr5:54170200-54170800	Enhancers	NHEK	skin
22	chr5:54170200-54171000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:54170200-54171200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr5:54170200-54171200	Enhancers	Fetal Lung	lung
25	chr5:54170200-54171400	Enhancers	Primary hematopoietic stem cells	blood
26	chr5:54170200-54171400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:54170200-54171400	Enhancers	Stomach Mucosa	stomach
28	chr5:54170200-54172400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:54170200-54172400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:54170400-54170800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:54170600-54171200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:54170600-54172400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:54170600-54172600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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