Variant report

Variant	rs60885323
Chromosome Location	chr17:19548174-19548175
allele	C/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	chr17:19547638-19548346	MCF-7	breast:	n/a	chr17:19547995-19548007
2	ESR1	chr17:19547747-19548191	T-47D	breast:	n/a	n/a
3	GATA3	chr17:19547747-19548198	T-47D	breast:	n/a	chr17:19547995-19548007
4	GATA3	chr17:19547632-19548255	MCF-7	breast:	n/a	chr17:19547995-19548007
5	ESR1	chr17:19547744-19548187	T-47D	breast:	n/a	n/a
6	CTCF	chr17:19547863-19549782	A549	lung:	n/a	n/a
7	FOS	chr17:19547798-19548476	MCF10A-Er-Src	breast:	n/a	n/a
8	ESR1	chr17:19547780-19548216	T-47D	breast:	n/a	n/a
9	FOS	chr17:19547754-19548526	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr17:19547945-19548424	MCF10A-Er-Src	breast:	n/a	n/a
11	EP300	chr17:19547837-19548494	Hela-S3	cervix:	n/a	n/a
12	ESR1	chr17:19547771-19548215	T-47D	breast:	n/a	n/a
13	RCOR1	chr17:19548051-19548369	Hela-S3	cervix:	n/a	n/a
14	MYC	chr17:19547839-19548457	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr17:19547806-19548543	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr17:19547778-19548494	Hela-S3	cervix:	n/a	chr17:19548084-19548092
17	GATA3	chr17:19547760-19548181	T-47D	breast:	n/a	chr17:19547995-19548007

Variant related genes	Relation type
ALDH3A2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs57341889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57366502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57430594	1.00[EUR][1000 genomes]
rs57657974	1.00[AMR][1000 genomes]
rs59551505	0.87[AMR][1000 genomes]
rs59919790	1.00[AMR][1000 genomes]
rs59986676	1.00[EUR][1000 genomes]
rs61397315	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7342960	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981556	1.00[AMR][1000 genomes]
rs73981565	1.00[AMR][1000 genomes]
rs73981567	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981569	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981572	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981592	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73981599	1.00[EUR][1000 genomes]
rs73981601	1.00[EUR][1000 genomes]
rs8065688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19538000-19549400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:19545000-19548800	Enhancers	Hela-S3	cervix
3	chr17:19545200-19548600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr17:19545400-19549600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:19545600-19550400	Enhancers	HepG2	liver
6	chr17:19545800-19550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:19546000-19549800	Weak transcription	HMEC	breast
8	chr17:19546200-19550400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr17:19546400-19548800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr17:19546400-19549400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:19546800-19548200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr17:19546800-19548800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr17:19547000-19549000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr17:19547000-19549000	Enhancers	A549	lung
15	chr17:19547000-19550200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:19547200-19549400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:19547400-19551800	Flanking Active TSS	Liver	Liver
18	chr17:19547600-19548200	Enhancers	Fetal Intestine Large	intestine
19	chr17:19547600-19548600	Enhancers	NHEK	skin
20	chr17:19547600-19550200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:19547800-19548200	Weak transcription	Placenta	Placenta
22	chr17:19548000-19548200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr17:19548000-19548200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:19548000-19548400	Enhancers	Fetal Intestine Small	intestine
25	chr17:19548000-19551000	Enhancers	Stomach Mucosa	stomach

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