Variant report

Variant	rs6582089
Chromosome Location	chr12:72666391-72666392
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	MAX	chr12:72665637-72666574	ECC-1	luminal epithelium:	n/a	chr12:72666392-72666402
2	REST	chr12:72664525-72667545	H1-neurons	neurons:	n/a	n/a
3	MAX	chr12:72665192-72666462	H1-hESC	embryonic stem cell:	n/a	chr12:72666392-72666402
4	CHD1	chr12:72664483-72669298	IMR90	lung:	n/a	chr12:72665403-72665413 chr12:72666399-72666409
5	POLR2A	chr12:72664488-72667607	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr12:72665866-72666442	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr12:72665033-72667943	H1-neurons	neurons:	n/a	n/a
8	TAF1	chr12:72665518-72666501	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr12:72666380-72666530	NHDF-neo	bronchial:	n/a	n/a
10	MAZ	chr12:72665018-72668139	IMR90	lung:	n/a	chr12:72666392-72666402 chr12:72667571-72667581
11	TCF12	chr12:72665794-72666650	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr12:72665174-72666439	H1-hESC	embryonic stem cell:	n/a	chr12:72666392-72666402
13	E2F6	chr12:72665148-72667189	H1-hESC	embryonic stem cell:	n/a	chr12:72666312-72666326 chr12:72666394-72666406 chr12:72666394-72666403
14	MAX	chr12:72665408-72666820	ECC-1	luminal epithelium:	n/a	chr12:72666392-72666402
15	ZBTB7A	chr12:72665895-72666548	ECC-1	luminal epithelium:	n/a	n/a
16	EP300	chr12:72665561-72666419	ECC-1	luminal epithelium:	n/a	chr12:72666373-72666389
17	MXI1	chr12:72664946-72668220	IMR90	lung:	n/a	n/a
18	ZBTB7A	chr12:72665869-72666792	ECC-1	luminal epithelium:	n/a	n/a
19	CTBP2	chr12:72665112-72668036	H1-hESC	embryonic stem cell:	n/a	n/a
20	SIN3A	chr12:72665140-72667917	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr12:72665179-72667322	HCT-116	colon:	n/a	chr12:72666392-72666402
22	POLR2A	chr12:72665080-72667402	H1-neurons	neurons:	n/a	n/a
23	TAF1	chr12:72665703-72666553	ECC-1	luminal epithelium:	n/a	n/a
24	E2F6	chr12:72665165-72667274	H1-hESC	embryonic stem cell:	n/a	chr12:72666312-72666326 chr12:72666394-72666406 chr12:72666394-72666403
25	ZNF143	chr12:72665140-72666748	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:72664308..72665953-chr12:72666174..72668987,2	MCF-7	breast:

Variant related genes	Relation type
TRHDE	TF binding region
TRHDE-AS1	TF binding region
ENSG00000236333	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10735967	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11179133	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11179147	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12820598	0.81[ASN][1000 genomes]
rs4144730	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4237862	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4237863	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4277155	0.85[EUR][1000 genomes]
rs4337081	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4384414	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4512894	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4589346	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4598709	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760826	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6582088	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7314135	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972362	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9668174	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832452	chr12:72584971-72764495	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv559362	chr12:72641784-72694691	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72663000-72668400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:72663200-72667600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:72663200-72670200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:72663200-72671200	Active TSS	NH-A	brain
5	chr12:72663400-72666600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr12:72663400-72667000	Active TSS	Brain Angular Gyrus	brain
7	chr12:72663400-72667400	Active TSS	Fetal Kidney	kidney
8	chr12:72663400-72667600	Active TSS	NHDF-Ad	bronchial
9	chr12:72663400-72667800	Active TSS	Ovary	ovary
10	chr12:72663400-72669400	Active TSS	Right Atrium	heart
11	chr12:72663600-72667200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:72664000-72667000	Active TSS	Brain Substantia Nigra	brain
13	chr12:72664600-72666600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr12:72664600-72667000	Active TSS	Brain Cingulate Gyrus	brain
15	chr12:72664600-72667200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
16	chr12:72664800-72666800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr12:72664800-72667800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:72664800-72667800	Active TSS	HMEC	breast
19	chr12:72664800-72668000	Bivalent/Poised TSS	NHLF	lung
20	chr12:72665000-72666600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:72665000-72666600	Active TSS	Brain Anterior Caudate	brain
22	chr12:72665000-72666800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:72665000-72666800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:72665000-72667800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr12:72665000-72667800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr12:72665000-72667800	Active TSS	Aorta	Aorta
27	chr12:72665000-72668000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr12:72665000-72668000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:72665000-72668200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:72665000-72668200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:72665000-72668600	Bivalent/Poised TSS	Osteobl	bone
32	chr12:72665200-72666400	Flanking Active TSS	Liver	Liver
33	chr12:72665200-72666400	Bivalent/Poised TSS	HepG2	liver
34	chr12:72665200-72666600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:72665200-72666600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:72665200-72666600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
37	chr12:72665200-72666600	Active TSS	Placenta Amnion	Placenta Amnion
38	chr12:72665200-72667000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
39	chr12:72665200-72667400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr12:72665200-72667400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:72665200-72667400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
42	chr12:72665200-72667600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
43	chr12:72665200-72667800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:72665200-72667800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
45	chr12:72665200-72668000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr12:72665200-72668000	Bivalent/Poised TSS	HSMM	muscle
47	chr12:72665200-72668200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
48	chr12:72665400-72666400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
49	chr12:72665400-72666600	Bivalent/Poised TSS	Esophagus	oesophagus
50	chr12:72665400-72667000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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