Variant report

Variant	rs62556540
Chromosome Location	chr9:116859852-116859853
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	chr9:116859735-116860120	MCF-7	breast:	n/a	n/a
2	GATA3	chr9:116859734-116860229	MCF-7	breast:	n/a	n/a
3	ZBTB7A	chr9:116859806-116861390	ECC-1	luminal epithelium:	n/a	chr9:116861008-116861015
4	GATA3	chr9:116859740-116860096	T-47D	breast:	n/a	n/a
5	GATA2	chr9:116859731-116860162	SH-SY5Y	brain:	n/a	n/a
6	MAX	chr9:116859665-116860433	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr9:116859750-116860388	A549	lung:	n/a	n/a
8	MAX	chr9:116859688-116860270	ECC-1	luminal epithelium:	n/a	n/a
9	NFIC	chr9:116859794-116860961	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr9:116859766-116860959	ECC-1	luminal epithelium:	n/a	n/a
11	GATA3	chr9:116859754-116860094	T-47D	breast:	n/a	n/a
12	EP300	chr9:116859799-116860821	ECC-1	luminal epithelium:	n/a	n/a
13	ZNF263	chr9:116859582-116860745	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116637031..116639708-chr9:116859646..116861440,2	MCF-7	breast:

Variant related genes	Relation type
KIF12	TF binding region
ENSG00000157657	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13291169	1.00[ASN][1000 genomes]
rs13291434	1.00[ASN][1000 genomes]
rs13291749	1.00[ASN][1000 genomes]
rs13300086	1.00[ASN][1000 genomes]
rs13300798	1.00[ASN][1000 genomes]
rs1808630	1.00[ASN][1000 genomes]
rs35719524	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62556537	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62556538	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62560767	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62560772	1.00[ASN][1000 genomes]
rs7044780	1.00[EUR][1000 genomes]
rs7857688	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	nsv466514	chr9:116810890-116867054	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv615222	chr9:116810890-116867054	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
6	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
7	nsv466515	chr9:116814661-116867054	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv615223	chr9:116814661-116867054	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv528822	chr9:116815777-116867054	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv466516	chr9:116815777-116867054	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv466518	chr9:116815777-116867054	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv466519	chr9:116815777-116867054	Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv466520	chr9:116815777-116867054	Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv466521	chr9:116815777-116867054	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv466522	chr9:116815777-116867054	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv466523	chr9:116815777-116867054	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv471319	chr9:116815777-116867054	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
18	nsv615224	chr9:116815777-116867054	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
19	nsv466524	chr9:116826842-116867054	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv466525	chr9:116826842-116867054	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv615225	chr9:116826842-116867054	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
23	nsv893751	chr9:116846467-116874355	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv515856	chr9:116853797-116867054	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	esv3326630	chr9:116859356-116862304	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	esv3328680	chr9:116859781-116862229	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116858400-116860000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
2	chr9:116858800-116860200	Enhancers	HepG2	liver
3	chr9:116858800-116862200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr9:116859200-116860000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:116859200-116860200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
6	chr9:116859200-116860200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:116859200-116860200	Bivalent Enhancer	Brain Germinal Matrix	brain
8	chr9:116859200-116860600	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr9:116859400-116860000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr9:116859400-116860000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:116859400-116860000	Enhancers	Colonic Mucosa	Colon
12	chr9:116859400-116860000	Enhancers	Gastric	stomach
13	chr9:116859400-116860400	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr9:116859400-116860600	Bivalent Enhancer	Fetal Brain Male	brain
15	chr9:116859400-116861400	Active TSS	Fetal Kidney	kidney
16	chr9:116859400-116862200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr9:116859600-116860200	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:116859600-116860200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:116859600-116860200	Flanking Active TSS	Pancreas	Pancrea
20	chr9:116859600-116860200	Enhancers	Stomach Mucosa	stomach
21	chr9:116859600-116860400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr9:116859600-116861800	Bivalent Enhancer	Placenta	Placenta
23	chr9:116859800-116860000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:116859800-116860000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:116859800-116860000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
26	chr9:116859800-116860000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:116859800-116860000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:116859800-116860000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:116859800-116860000	Bivalent Enhancer	Adipose Nuclei	Adipose
30	chr9:116859800-116860000	Bivalent Enhancer	Brain Angular Gyrus	brain
31	chr9:116859800-116860000	Bivalent Enhancer	Brain Hippocampus Middle	brain
32	chr9:116859800-116860000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr9:116859800-116860000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:116859800-116860000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
35	chr9:116859800-116860000	Enhancers	Fetal Lung	lung
36	chr9:116859800-116860000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr9:116859800-116860000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr9:116859800-116860000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
39	chr9:116859800-116860200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr9:116859800-116860200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
41	chr9:116859800-116860200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:116859800-116860200	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
43	chr9:116859800-116860200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
44	chr9:116859800-116860200	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr9:116859800-116860200	Flanking Active TSS	A549	lung
46	chr9:116859800-116860200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
47	chr9:116859800-116860400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:116859800-116860400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr9:116859800-116860400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
50	chr9:116859800-116860400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--

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