Variant report

Variant	rs62538957
Chromosome Location	chr9:12680607-12680608
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	TEAD4	chr9:12680275-12680809	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr9:12680244-12680809	SK-N-SH	brain:	n/a	n/a
3	TEAD4	chr9:12680291-12680848	ECC-1	luminal epithelium:	n/a	n/a
4	GATA3	chr9:12680252-12680725	MCF-7	breast:	n/a	n/a
5	TEAD4	chr9:12680424-12680766	H1-hESC	embryonic stem cell:	n/a	n/a
6	GATA3	chr9:12680226-12680687	T-47D	breast:	n/a	n/a
7	GATA3	chr9:12680272-12680798	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr9:12680221-12680683	T-47D	breast:	n/a	n/a
9	POLR2A	chr9:12680382-12680792	SK-N-MC	brain:	n/a	n/a
10	GATA3	chr9:12680244-12680691	SK-N-SH	brain:	n/a	n/a
11	EP300	chr9:12680294-12680793	T-47D	breast:	n/a	chr9:12680540-12680554 chr9:12680534-12680548 chr9:12680542-12680556

Variant related genes	Relation type
TYRP1	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16929342	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16929345	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16929346	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16929347	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34746817	0.86[AFR][1000 genomes]
rs4289906	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58345121	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59334502	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62538946	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62538947	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62538950	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62538951	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62538952	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62538954	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62538955	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62538956	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62538958	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62538959	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62540170	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62540172	0.94[AFR][1000 genomes]
rs62542903	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62542904	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62542905	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7039726	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7847593	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7847837	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7852946	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7875119	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7875466	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892558	chr9:12178984-12687872	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1027260	chr9:12196141-12709959	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv540062	chr9:12196141-12709959	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv831513	chr9:12531673-12695747	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv892572	chr9:12549675-12715816	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1016570	chr9:12576095-12722387	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv466255	chr9:12628213-12699776	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv613611	chr9:12628213-12699776	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv466256	chr9:12628213-12712157	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv613612	chr9:12628213-12712157	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv613613	chr9:12641987-12773263	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv466257	chr9:12671693-12692364	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv613614	chr9:12671693-12692364	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12676400-12681000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:12679800-12682200	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr9:12680000-12680800	Enhancers	Fetal Lung	lung
4	chr9:12680000-12680800	Enhancers	A549	lung
5	chr9:12680000-12681000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:12680000-12681200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:12680000-12681600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:12680000-12681800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr9:12680200-12680800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr9:12680200-12681000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:12680200-12681000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:12680200-12681000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:12680200-12681200	Enhancers	NHEK	skin
14	chr9:12680200-12681400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr9:12680200-12681600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr9:12680200-12681600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:12680200-12682200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:12680200-12688200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:12680400-12681000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:12680400-12681400	Enhancers	HMEC	breast
21	chr9:12680600-12680800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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