Variant report

Variant	rs2019005
Chromosome Location	chr5:54170299-54170300
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	GATA3	chr5:54170162-54170821	MCF-7	breast:	n/a	n/a
2	FOS	chr5:54170270-54170642	MCF10A-Er-Src	breast:	n/a	chr5:54170619-54170631 chr5:54170305-54170315 chr5:54170305-54170315
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	EP300	chr5:54170149-54170891	T-47D	breast:	n/a	n/a
9	EP300	chr5:54170012-54170769	ECC-1	luminal epithelium:	n/a	n/a
10	FOXM1	chr5:54170005-54170708	ECC-1	luminal epithelium:	n/a	n/a
11	FOS	chr5:54170233-54170786	MCF10A-Er-Src	breast:	n/a	chr5:54170619-54170631 chr5:54170305-54170315 chr5:54170305-54170315
12	GATA3	chr5:54170276-54170847	T-47D	breast:	n/a	n/a
13	TFAP2C	chr5:54170251-54170702	Hela-S3	cervix:	n/a	n/a
14	TEAD4	chr5:54170254-54170640	ECC-1	luminal epithelium:	n/a	n/a
15	MAX	chr5:54170247-54170796	Hela-S3	cervix:	n/a	n/a
16	TCF7L2	chr5:54170163-54170640	MCF-7	breast:	n/a	n/a
17	GATA3	chr5:54170103-54170883	MCF-7	breast:	n/a	n/a
18	GATA3	chr5:54170214-54170870	T-47D	breast:	n/a	n/a
19	TEAD4	chr5:54170120-54170676	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr5:54170055-54170839	SK-N-MC	brain:	n/a	n/a
21	STAT3	chr5:54170252-54170737	MCF10A-Er-Src	breast:	n/a	chr5:54170641-54170649
22	EP300	chr5:54170170-54170808	Hela-S3	cervix:	n/a	n/a
23	NFIC	chr5:54170089-54170736	ECC-1	luminal epithelium:	n/a	n/a
24	CEBPB	chr5:54170171-54170837	ECC-1	luminal epithelium:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
25	TCF12	chr5:54170100-54170715	ECC-1	luminal epithelium:	n/a	n/a
26	BRCA1	chr5:54170238-54170757	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr5:54170137-54170859	Hela-S3	cervix:	n/a	chr5:54170638-54170649 chr5:54170639-54170650 chr5:54170638-54170651
28	STAT3	chr5:54170127-54170727	MCF10A-Er-Src	breast:	n/a	chr5:54170641-54170649
29	EP300	chr5:54170217-54170691	T-47D	breast:	n/a	n/a
30	TFAP2A	chr5:54170232-54170733	Hela-S3	cervix:	n/a	chr5:54170405-54170420
31	TCF7L2	chr5:54170009-54170825	Hela-S3	cervix:	n/a	n/a
32	EP300	chr5:54170098-54170672	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000249843	TF binding region
ENSG00000232517	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	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1005622	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10056452	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10058862	0.80[EUR][1000 genomes]
rs10805469	0.84[EUR][1000 genomes]
rs10805470	0.82[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];0.89[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];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940434	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11738151	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11742711	0.90[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	0.89[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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560166	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]
rs1560167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17588816	0.82[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];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2195392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[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];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564901	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2897758	0.89[EUR][1000 genomes]
rs3916738	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3935813	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4242047	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	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4502767	0.90[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	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865881	0.99[ASN][1000 genomes]
rs4865882	0.93[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	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7709516	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs976645	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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54168400-54170400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:54168400-54171800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:54168600-54175600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:54169000-54171000	Enhancers	HUVEC	blood vessel
5	chr5:54169200-54170600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:54169400-54171000	Enhancers	Osteobl	bone
7	chr5:54169400-54171400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:54169400-54171800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:54169600-54171000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:54169600-54171000	Enhancers	Adipose Nuclei	Adipose
11	chr5:54169600-54171400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr5:54169600-54171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:54169600-54171400	Enhancers	Hela-S3	cervix
14	chr5:54169800-54170800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:54169800-54171000	Enhancers	Liver	Liver
16	chr5:54169800-54171200	Weak transcription	Left Ventricle	heart
17	chr5:54170000-54170400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:54170000-54171200	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr5:54170000-54171400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr5:54170000-54171400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr5:54170000-54171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:54170000-54178800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:54170200-54170400	Enhancers	NHLF	lung
24	chr5:54170200-54170600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:54170200-54170800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr5:54170200-54170800	Enhancers	NHEK	skin
27	chr5:54170200-54171000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:54170200-54171200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:54170200-54171200	Enhancers	Fetal Lung	lung
30	chr5:54170200-54171400	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:54170200-54171400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:54170200-54171400	Enhancers	Stomach Mucosa	stomach
33	chr5:54170200-54172400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:54170200-54172400	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links