Variant report

Variant	rs62530325
Chromosome Location	chr9:976874-976875
allele	C/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	CTCF	chr9:976760-976910	WERI-Rb-1	eye:	n/a	n/a
2	KAP1	chr9:976800-977251	HEK293	kidney:	n/a	n/a
3	ZNF263	chr9:975708-978049	HEK293-T-REx	kidney:	n/a	n/a
4	ZNF143	chr9:976287-977114	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr9:976862-977338	ECC-1	luminal epithelium:	n/a	n/a
6	SUZ12	chr9:974936-978765	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr9:976450-977341	H1-hESC	embryonic stem cell:	n/a	chr9:976702-976712
8	YY1	chr9:976799-977253	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr9:976288-977241	ECC-1	luminal epithelium:	n/a	chr9:976332-976342 chr9:976440-976450
10	MAX	chr9:976598-977436	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTBP2	chr9:975752-978187	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF12	chr9:976641-977046	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr9:976184-977298	H1-hESC	embryonic stem cell:	n/a	chr9:976332-976342 chr9:976440-976450
14	TBP	chr9:976238-977167	H1-hESC	embryonic stem cell:	n/a	n/a
15	EGR1	chr9:976631-977630	H1-hESC	embryonic stem cell:	n/a	chr9:976990-977000 chr9:977491-977501
16	SUZ12	chr9:972157-978361	NT2-D1	testis:	n/a	n/a
17	GABPA	chr9:976605-976939	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr9:975227-977526	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr9:976601-977307	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr9:976228-977383	ECC-1	luminal epithelium:	n/a	chr9:976332-976342 chr9:976440-976450
21	E2F6	chr9:976591-977334	H1-hESC	embryonic stem cell:	n/a	chr9:976702-976712
22	SIN3A	chr9:976266-977176	H1-hESC	embryonic stem cell:	n/a	chr9:976742-976753

Variant related genes	Relation type
DMRT3	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs279885	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs279887	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs279888	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs279889	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs279909	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs399000	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs454101	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56265015	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025492	chr9:478813-1157169	Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv539897	chr9:478813-1157169	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv429977	chr9:584087-983301	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv613037	chr9:643453-1138368	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817248	chr9:706283-1457665	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv892010	chr9:841152-1069663	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1034070	chr9:911265-1152351	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2755928	chr9:924525-985979	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv892013	chr9:943611-1047343	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1018926	chr9:965006-1014141	Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv892014	chr9:972476-1032153	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3408115	chr9:975477-978825	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:974400-977800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr9:975400-978800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:975600-977400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:975800-977400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:976000-977200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
6	chr9:976000-977200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
7	chr9:976000-977200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
8	chr9:976000-977600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr9:976000-977600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr9:976000-977600	Bivalent/Poised TSS	Fetal Brain Female	brain
11	chr9:976000-977600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
12	chr9:976000-977800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr9:976000-977800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr9:976000-977800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:976000-977800	Bivalent Enhancer	Fetal Stomach	stomach
16	chr9:976200-977000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:976200-977200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:976200-977200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:976200-977200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
20	chr9:976200-977200	Bivalent/Poised TSS	A549	lung
21	chr9:976200-977200	Bivalent/Poised TSS	HSMM	muscle
22	chr9:976200-977400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:976200-977400	Enhancers	Pancreas	Pancrea
24	chr9:976200-977400	Flanking Bivalent TSS/Enh	Right Ventricle	heart
25	chr9:976200-977800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:976200-977800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:976200-977800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr9:976200-977800	Bivalent Enhancer	Fetal Brain Male	brain
29	chr9:976200-977800	Bivalent Enhancer	Spleen	Spleen
30	chr9:976200-978000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr9:976400-977000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
32	chr9:976400-977200	Active TSS	Aorta	Aorta
33	chr9:976400-977200	Enhancers	Gastric	stomach
34	chr9:976400-977400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr9:976400-977400	Bivalent/Poised TSS	Esophagus	oesophagus
36	chr9:976400-977400	Bivalent Enhancer	Left Ventricle	heart
37	chr9:976400-977400	Bivalent Enhancer	Ovary	ovary
38	chr9:976400-977800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:976400-977800	Bivalent Enhancer	Lung	lung
40	chr9:976400-978000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
41	chr9:976400-978600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
42	chr9:976600-977000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
43	chr9:976600-977000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
44	chr9:976600-977200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:976600-977200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:976600-977200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr9:976600-977200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:976600-977200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:976600-977200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
50	chr9:976600-977400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle

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