Variant report

Variant	rs539079354
Chromosome Location	chr12:57853004-57853005
allele	A/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	CTCF	chr12:57852920-57853070	GM12868	blood:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
2	POLR2A	chr12:57852558-57853696	SK-N-MC	brain:	n/a	n/a
3	CTCF	chr12:57852904-57853206	MCF-7	breast:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
4	CTCF	chr12:57852940-57853090	HCM	heart:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
5	FOXA1	chr12:57852952-57853230	T-47D	breast:	n/a	n/a
6	MYC	chr12:57852693-57853653	K562	blood:	n/a	n/a
7	SP1	chr12:57852528-57856905	A549	lung:	n/a	chr12:57855088-57855100 chr12:57854788-57854797 chr12:57855421-57855430 chr12:57854019-57854032 chr12:57856662-57856671 chr12:57855543-57855552 chr12:57855232-57855244 chr12:57855089-57855099 chr12:57855429-57855443 chr12:57855571-57855580 chr12:57854556-57854565 chr12:57855541-57855553 chr12:57853860-57853872 chr12:57854024-57854036 chr12:57855089-57855098 chr12:57855570-57855582 chr12:57856000-57856009 chr12:57853899-57853911 chr12:57854788-57854797 chr12:57855233-57855247 chr12:57856151-57856163 chr12:57856152-57856161 chr12:57855594-57855608 chr12:57855090-57855099 chr12:57855547-57855561 chr12:57856000-57856014 chr12:57855999-57856011 chr12:57853861-57853871 chr12:57854546-57854560 chr12:57855232-57855244 chr12:57853861-57853870 chr12:57855570-57855582 chr12:57856152-57856166 chr12:57853659-57853668 chr12:57855567-57855581 chr12:57855572-57855581 chr12:57855542-57855551 chr12:57853154-57853161 chr12:57854024-57854036 chr12:57856153-57856162 chr12:57855090-57855099 chr12:57856001-57856010 chr12:57855085-57855099 chr12:57856525-57856539 chr12:57856151-57856163 chr12:57854788-57854798 chr12:57855999-57856011 chr12:57854025-57854034 chr12:57853836-57853850 chr12:57856152-57856162 chr12:57855232-57855243 chr12:57854021-57854035 chr12:57855114-57855127 chr12:57853901-57853910 chr12:57855089-57855099 chr12:57855088-57855100 chr12:57855950-57855964 chr12:57856000-57856010 chr12:57855543-57855552 chr12:57854557-57854566
8	POLR2A	chr12:57852195-57853555	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:57852527-57853046	GM12878	blood:	n/a	n/a
10	RAD21	chr12:57852623-57853764	HCT-116	colon:	n/a	chr12:57853738-57853752 chr12:57853045-57853059 chr12:57853044-57853063 chr12:57853354-57853373
11	CTCF	chr12:57852960-57853110	GM12864	blood:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
12	MXI1	chr12:57852894-57853722	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:57852714-57853310	K562	blood:	n/a	n/a
14	SIN3AK20	chr12:57852936-57853687	PANC-1	pancreas:	n/a	n/a
15	NFIC	chr12:57852570-57853849	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr12:57852980-57853130	GM12865	blood:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
17	CTCF	chr12:57852790-57853281	H1-hESC	embryonic stem cell:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
18	RAD21	chr12:57852869-57853198	SK-N-SH_RA	brain:	n/a	chr12:57853045-57853059 chr12:57853044-57853063
19	RUNX3	chr12:57852648-57853698	GM12878	blood:	n/a	chr12:57853295-57853304 chr12:57853183-57853200 chr12:57853288-57853303 chr12:57853295-57853304
20	CTCF	chr12:57852980-57853130	Caco-2	colon:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
21	CTCF	chr12:57852920-57853070	BE2_C	brain:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
22	ZNF143	chr12:57852710-57853539	GM12878	blood:	n/a	n/a
23	SIN3AK20	chr12:57852949-57853216	HepG2	liver:	n/a	n/a
24	RAD21	chr12:57852850-57853231	K562	blood:	n/a	chr12:57853045-57853059 chr12:57853044-57853063
25	MAX	chr12:57852765-57853790	K562	blood:	n/a	n/a
26	ZBTB7A	chr12:57852790-57854062	K562	blood:	n/a	n/a
27	EP300	chr12:57852649-57853396	GM12878	blood:	n/a	n/a
28	ZBTB7A	chr12:57852886-57853169	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:57852552-57853473	Hela-S3	cervix:	n/a	n/a
30	SP1	chr12:57852559-57853865	HCT-116	colon:	n/a	chr12:57853659-57853668 chr12:57853154-57853161 chr12:57853836-57853850
31	CTCF	chr12:57852767-57853236	K562	blood:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
32	NFE2	chr12:57852718-57853100	GM12878	blood:	n/a	n/a
33	CTCF	chr12:57852940-57853090	HEK293	kidney:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
34	POLR2A	chr12:57852571-57853344	GM15510	blood:	n/a	n/a
35	ARID3A	chr12:57852875-57853214	HepG2	liver:	n/a	n/a
36	MAZ	chr12:57852663-57853735	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr12:57852834-57853202	GM19239	blood:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
38	RFX5	chr12:57852661-57853186	GM12878	blood:	n/a	chr12:57852885-57852899 chr12:57852887-57852896
39	POLR2A	chr12:57852638-57853736	HUVEC	blood vessel:	n/a	n/a
40	CREB1	chr12:57852771-57853808	A549	lung:	n/a	n/a
41	CTCF	chr12:57852860-57853010	WI-38	lung:	n/a	n/a
42	RUNX3	chr12:57852762-57853700	GM12878	blood:	n/a	chr12:57853295-57853304 chr12:57853183-57853200 chr12:57853288-57853303 chr12:57853295-57853304
43	SIN3AK20	chr12:57852832-57853644	A549	lung:	n/a	n/a
44	CTCF	chr12:57852940-57853090	NHLF	lung:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
45	RAD21	chr12:57852783-57853304	MCF-7	breast:	n/a	chr12:57853045-57853059 chr12:57853044-57853063
46	CTCF	chr12:57852980-57853130	HepG2	liver:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060
47	STAT5A	chr12:57852780-57853526	K562	blood:	n/a	chr12:57853437-57853449
48	POLR2A	chr12:57852633-57853084	GM12891	blood:	n/a	n/a
49	RAD21	chr12:57852773-57853296	ECC-1	luminal epithelium:	n/a	chr12:57853045-57853059 chr12:57853044-57853063
50	CTCF	chr12:57852980-57853130	GM12872	blood:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853044-57853060

No.	Distal block	Cell Line	Cell type
1	chr12:57852621..57854513-chr12:58130296..58131944,2	K562	blood:
2	chr12:57852643..57853481-chr12:58176405..58177025,2	K562	blood:
3	chr12:57625841..57628130-chr12:57851805..57854009,2	K562	blood:
4	chr1:226186864..226187449-chr12:57852398..57853191,2	Hela-S3	cervix:
5	chr12:57849885..57859254-chr12:57908711..57915821,16	K562	blood:
6	chr12:57852367..57853297-chr18:2655179..2655859,2	Hela-S3	cervix:
7	chr12:57851014..57853081-chr12:57861682..57863559,2	K562	blood:
8	chr12:57622711..57625468-chr12:57850226..57853031,2	K562	blood:
9	chr12:57852555..57853055-chr3:33155341..33155929,2	Hela-S3	cervix:
10	chr12:57822750..57826133-chr12:57852904..57855936,4	K562	blood:
11	chr12:57693773..57695685-chr12:57852034..57854514,2	K562	blood:
12	chr12:57850914..57853325-chr12:57864861..57866988,3	K562	blood:
13	chr12:57852034..57858739-chr12:57911478..57917144,8	MCF-7	breast:
14	chr12:57852892..57855767-chr12:58158814..58160402,2	K562	blood:
15	chr12:57851728..57854572-chr12:58144859..58146430,2	MCF-7	breast:
16	chr12:57852567..57853136-chr12:58087060..58087719,2	MCF-7	breast:
17	chr12:57851512..57853202-chr12:57880450..57882200,2	K562	blood:
18	chr12:57851318..57853118-chr12:57916144..57917721,2	K562	blood:
19	chr12:57852790..57853327-chr12:58015168..58015867,2	MCF-7	breast:
20	chr12:57852282..57853274-chr14:74318374..74319293,2	Hela-S3	cervix:
21	chr12:57820715..57827591-chr12:57847165..57857509,18	K562	blood:
22	chr12:57848876..57851404-chr12:57851445..57853731,2	MCF-7	breast:
23	chr12:57850715..57853202-chr12:57880450..57882915,3	K562	blood:
24	chr12:57850154..57858218-chr12:57910899..57919538,20	K562	blood:

Variant related genes	Relation type
GLI1	TF binding region
ENSG00000258653	Chromatin interaction
ENSG00000266405	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000182199	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000170275	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000101596	Chromatin interaction
ENSG00000140043	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000111012	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 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
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv8974	chr12:57852779-57865881	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57852200-57853400	Flanking Active TSS	NHEK	skin
2	chr12:57852400-57853400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr12:57852400-57853400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:57852400-57853400	Flanking Active TSS	HSMMtube	muscle
5	chr12:57852400-57853600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr12:57852400-57853600	Flanking Active TSS	Dnd41	blood
7	chr12:57852400-57853600	Flanking Active TSS	HUVEC	blood vessel
8	chr12:57852400-57853800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr12:57852400-57853800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr12:57852400-57853800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:57852400-57853800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:57852400-57854600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr12:57852400-57856600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:57852400-57856800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr12:57852600-57853200	Flanking Active TSS	Colonic Mucosa	Colon
16	chr12:57852600-57853400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:57852600-57853400	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr12:57852600-57853400	Flanking Active TSS	Liver	Liver
19	chr12:57852600-57853400	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr12:57852600-57853400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr12:57852600-57853400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr12:57852600-57853400	Flanking Active TSS	Stomach Mucosa	stomach
23	chr12:57852600-57853400	Flanking Active TSS	HMEC	breast
24	chr12:57852600-57853800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:57852600-57853800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr12:57852600-57854200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr12:57852600-57854200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:57852600-57854600	Active TSS	Psoas Muscle	Psoas
29	chr12:57852600-57856600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr12:57852600-57856600	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr12:57852800-57853200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:57852800-57853200	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr12:57852800-57853200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:57852800-57853200	Active TSS	Monocytes-CD14+_RO01746	blood
35	chr12:57852800-57853400	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr12:57852800-57853600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:57852800-57853800	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr12:57852800-57853800	Active TSS	Esophagus	oesophagus
39	chr12:57852800-57853800	Active TSS	Lung	lung
40	chr12:57852800-57853800	Active TSS	Placenta Amnion	Placenta Amnion
41	chr12:57852800-57853800	Active TSS	Spleen	Spleen
42	chr12:57852800-57853800	Active TSS	NHDF-Ad	bronchial
43	chr12:57852800-57854000	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr12:57852800-57854000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:57852800-57854000	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr12:57852800-57854000	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr12:57852800-57854200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:57852800-57854200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:57852800-57854200	Active TSS	Primary T cells from cord blood	blood
50	chr12:57852800-57854200	Active TSS	Pancreatic Islets	Pancreatic Islet

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