Variant report

Variant	rs507562
Chromosome Location	chr12:57849768-57849769
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	MAX	chr12:57848249-57850285	K562	blood:	n/a	chr12:57848384-57848393 chr12:57848860-57848869
2	POLR2A	chr12:57848247-57850539	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:57848172-57850954	H1-hESC	embryonic stem cell:	n/a	n/a
4	BCL3	chr12:57849328-57850197	A549	lung:	n/a	n/a
5	TCF12	chr12:57849724-57850395	A549	lung:	n/a	n/a
6	TCF12	chr12:57848239-57850301	ECC-1	luminal epithelium:	n/a	chr12:57848996-57849003 chr12:57849063-57849070
7	HCFC1	chr12:57848060-57850406	Hela-S3	cervix:	n/a	n/a
8	USF2	chr12:57849481-57849846	Hela-S3	cervix:	n/a	n/a
9	MYC	chr12:57849684-57850256	K562	blood:	n/a	n/a
10	E2F6	chr12:57849609-57850366	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3A	chr12:57848509-57850295	H1-hESC	embryonic stem cell:	n/a	chr12:57848921-57848931
12	ELF1	chr12:57849700-57850547	GM12878	blood:	n/a	n/a
13	HEY1	chr12:57848277-57850326	K562	blood:	n/a	n/a
14	ZNF263	chr12:57849416-57850269	HEK293-T-REx	kidney:	n/a	n/a
15	POLR2A	chr12:57848357-57850243	HepG2	liver:	n/a	n/a
16	CTCF	chr12:57849580-57850495	SK-N-SH	brain:	n/a	n/a
17	MAX	chr12:57849608-57850326	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:57848252-57850408	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:57848438-57850217	Raji	blood:	n/a	n/a
20	TAF1	chr12:57849761-57850281	H1-hESC	embryonic stem cell:	n/a	n/a
21	BHLHE40	chr12:57849577-57850156	K562	blood:	n/a	n/a
22	CTCF	chr12:57849762-57850319	MCF-7	breast:	n/a	n/a
23	MAX	chr12:57848241-57850323	ECC-1	luminal epithelium:	n/a	chr12:57848384-57848393 chr12:57848860-57848869
24	E2F6	chr12:57849677-57850263	A549	lung:	n/a	n/a
25	POLR2A	chr12:57848664-57850795	K562	blood:	n/a	n/a
26	MAZ	chr12:57848291-57849805	IMR90	lung:	n/a	chr12:57848384-57848393 chr12:57848860-57848869
27	CTCF	chr12:57849640-57849790	GM12871	blood:	n/a	n/a
28	MAX	chr12:57848307-57850323	ECC-1	luminal epithelium:	n/a	chr12:57848384-57848393 chr12:57848860-57848869
29	E2F6	chr12:57849661-57850314	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr12:57848200-57851732	A549	lung:	n/a	chr12:57849041-57849048 chr12:57848972-57848985
31	MAZ	chr12:57848277-57850253	K562	blood:	n/a	chr12:57848384-57848393 chr12:57848860-57848869
32	POLR2A	chr12:57849516-57849776	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr12:57849766-57849845	GM12878	blood:	n/a	n/a
34	MYC	chr12:57848257-57850231	K562	blood:	n/a	chr12:57848384-57848393 chr12:57848860-57848869
35	KAP1	chr12:57849340-57850354	HEK293	kidney:	n/a	n/a
36	POLR2A	chr12:57848252-57850238	ECC-1	luminal epithelium:	n/a	n/a
37	JUN	chr12:57848001-57851107	K562	blood:	n/a	chr12:57848382-57848395
38	MAX	chr12:57849625-57850387	A549	lung:	n/a	n/a
39	MAX	chr12:57849586-57850238	K562	blood:	n/a	n/a
40	RAD21	chr12:57849722-57850380	A549	lung:	n/a	chr12:57849795-57849807
41	CTCF	chr12:57849620-57849770	GM12866	blood:	n/a	n/a
42	MYC	chr12:57849744-57850235	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:57848244-57850357	K562	blood:	n/a	n/a
44	JUND	chr12:57849474-57850306	K562	blood:	n/a	n/a
45	MAX	chr12:57849718-57850333	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57702958..57705932-chr12:57847921..57850927,4	K562	blood:
2	chr12:57503986..57506964-chr12:57847315..57851029,3	K562	blood:
3	chr12:57848182..57850484-chr12:57880307..57884604,3	K562	blood:
4	chr12:57687373..57690350-chr12:57849601..57852128,3	K562	blood:
5	chr12:57848732..57851043-chr12:57853897..57856236,2	MCF-7	breast:
6	chr12:57822102..57825804-chr12:57846903..57851131,6	MCF-7	breast:
7	chr12:57846927..57848527-chr12:57849193..57850926,2	MCF-7	breast:
8	chr12:57671280..57675750-chr12:57846169..57850162,4	K562	blood:
9	chr12:57848374..57850176-chr12:57916596..57918121,2	MCF-7	breast:
10	chr12:57843448..57846710-chr12:57847033..57851571,4	MCF-7	breast:
11	chr12:57821945..57831494-chr12:57839441..57852842,32	K562	blood:
12	chr12:57820715..57827591-chr12:57847165..57857509,18	K562	blood:

Variant related genes	Relation type
GLI1	TF binding region
ENSG00000123329	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000258830	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000175189	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000166888	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11172142	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11172155	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs11830804	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs12227309	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2943691	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2943692	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2943693	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs473465	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs487722	0.84[ASN][1000 genomes]
rs538548	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs567895	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs568793	0.80[JPT][hapmap]
rs7297282	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7302906	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs9738646	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57843600-57850400	Enhancers	Fetal Intestine Large	intestine
2	chr12:57844000-57850400	Enhancers	Fetal Intestine Small	intestine
3	chr12:57846800-57849800	Weak transcription	Pancreas	Pancrea
4	chr12:57846800-57849800	Weak transcription	Right Ventricle	heart
5	chr12:57846800-57849800	Weak transcription	Osteobl	bone
6	chr12:57846800-57852200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:57846800-57852200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:57846800-57852600	Weak transcription	Fetal Lung	lung
9	chr12:57846800-57852600	Weak transcription	Left Ventricle	heart
10	chr12:57846800-57852600	Weak transcription	Right Atrium	heart
11	chr12:57846800-57852600	Weak transcription	NHDF-Ad	bronchial
12	chr12:57847200-57849800	Weak transcription	Primary B cells from cord blood	blood
13	chr12:57847800-57852600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:57848200-57849800	Enhancers	Fetal Muscle Leg	muscle
15	chr12:57848200-57850200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr12:57848400-57849800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:57848400-57849800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:57848400-57849800	Enhancers	HSMM	muscle
19	chr12:57848400-57850000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:57848400-57850200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:57848400-57852200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:57848600-57849800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr12:57848600-57850000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:57848600-57850000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr12:57848600-57850000	Flanking Active TSS	A549	lung
26	chr12:57848600-57850600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr12:57848600-57850800	Flanking Active TSS	K562	blood
28	chr12:57848600-57851200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr12:57848800-57849800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:57848800-57850400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:57848800-57850400	Enhancers	Psoas Muscle	Psoas
32	chr12:57848800-57852200	Weak transcription	Dnd41	blood
33	chr12:57848800-57852600	Active TSS	Liver	Liver
34	chr12:57849000-57849800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:57849000-57850200	Active TSS	H9 Cell Line	embryonic stem cell
36	chr12:57849000-57850400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr12:57849000-57850400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:57849000-57850600	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr12:57849000-57850600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr12:57849000-57850600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr12:57849000-57850600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr12:57849200-57850000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:57849200-57850200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:57849200-57850400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:57849200-57850400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:57849200-57850400	Enhancers	Fetal Heart	heart
47	chr12:57849200-57850600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr12:57849200-57852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:57849400-57849800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr12:57849400-57849800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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