Variant report

Variant	rs541371501
Chromosome Location	chr12:57853437-57853438
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	POLR2A	chr12:57852558-57853696	SK-N-MC	brain:	n/a	n/a
2	FOSL2	chr12:57853263-57853527	A549	lung:	n/a	n/a
3	MYC	chr12:57852693-57853653	K562	blood:	n/a	n/a
4	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
5	POLR2A	chr12:57852195-57853555	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr12:57852623-57853764	HCT-116	colon:	n/a	chr12:57853738-57853752 chr12:57853045-57853059 chr12:57853044-57853063 chr12:57853354-57853373
7	E2F6	chr12:57853369-57853832	K562	blood:	n/a	chr12:57853730-57853739
8	MXI1	chr12:57852894-57853722	HepG2	liver:	n/a	n/a
9	SIN3AK20	chr12:57852936-57853687	PANC-1	pancreas:	n/a	n/a
10	NFIC	chr12:57852570-57853849	ECC-1	luminal epithelium:	n/a	n/a
11	RUNX3	chr12:57852648-57853698	GM12878	blood:	n/a	chr12:57853295-57853304 chr12:57853183-57853200 chr12:57853288-57853303 chr12:57853295-57853304
12	REST	chr12:57853318-57853579	SK-N-SH	brain:	n/a	n/a
13	YY1	chr12:57853320-57853649	SK-N-SH_RA	brain:	n/a	n/a
14	ZNF143	chr12:57852710-57853539	GM12878	blood:	n/a	n/a
15	MAX	chr12:57852765-57853790	K562	blood:	n/a	n/a
16	ZBTB7A	chr12:57852790-57854062	K562	blood:	n/a	n/a
17	POLR2A	chr12:57852552-57853473	Hela-S3	cervix:	n/a	n/a
18	SP1	chr12:57852559-57853865	HCT-116	colon:	n/a	chr12:57853659-57853668 chr12:57853154-57853161 chr12:57853836-57853850
19	MAZ	chr12:57852663-57853735	Hela-S3	cervix:	n/a	n/a
20	HDAC2	chr12:57853332-57853670	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:57852638-57853736	HUVEC	blood vessel:	n/a	n/a
22	CREB1	chr12:57852771-57853808	A549	lung:	n/a	n/a
23	RUNX3	chr12:57852762-57853700	GM12878	blood:	n/a	chr12:57853295-57853304 chr12:57853183-57853200 chr12:57853288-57853303 chr12:57853295-57853304
24	SIN3AK20	chr12:57852832-57853644	A549	lung:	n/a	n/a
25	STAT5A	chr12:57852780-57853526	K562	blood:	n/a	chr12:57853437-57853449
26	CTCF	chr12:57853340-57853490	AG10803	skin:	n/a	chr12:57853355-57853376
27	RAD21	chr12:57852614-57853632	HCT-116	colon:	n/a	chr12:57853045-57853059 chr12:57853044-57853063 chr12:57853354-57853373
28	ELK1	chr12:57852652-57853546	GM12878	blood:	n/a	n/a
29	MAX	chr12:57852581-57853843	ECC-1	luminal epithelium:	n/a	n/a
30	UBTF	chr12:57852875-57853621	K562	blood:	n/a	n/a
31	USF2	chr12:57852633-57853439	Hela-S3	cervix:	n/a	n/a
32	MAX	chr12:57852738-57853664	GM12878	blood:	n/a	n/a
33	KAP1	chr12:57852651-57853476	HEK293	kidney:	n/a	n/a
34	CREB1	chr12:57852789-57853758	ECC-1	luminal epithelium:	n/a	n/a
35	STAT1	chr12:57852938-57853683	GM12878	blood:	n/a	chr12:57853437-57853449 chr12:57853591-57853603
36	YY1	chr12:57853280-57853669	SK-N-SH	brain:	n/a	n/a
37	NFIC	chr12:57852912-57853716	GM12878	blood:	n/a	n/a
38	RFX5	chr12:57852894-57853528	HepG2	liver:	n/a	n/a
39	FOSL2	chr12:57852567-57853743	A549	lung:	n/a	n/a
40	YY1	chr12:57853406-57853575	HCT-116	colon:	n/a	n/a
41	MXI1	chr12:57852694-57853625	H1-hESC	embryonic stem cell:	n/a	n/a
42	ELF1	chr12:57852790-57853774	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:57852811-57853639	HCT-116	colon:	n/a	n/a
44	CTCF	chr12:57852785-57853505	IMR90	lung:	n/a	chr12:57853045-57853066 chr12:57853046-57853059 chr12:57853043-57853061 chr12:57853355-57853376 chr12:57853044-57853060
45	MAX	chr12:57853300-57853629	K562	blood:	n/a	n/a
46	POLR2A	chr12:57852567-57853631	HCT-116	colon:	n/a	n/a
47	POLR2A	chr12:57852687-57853614	SK-N-MC	brain:	n/a	n/a
48	YY1	chr12:57852930-57853606	A549	lung:	n/a	n/a
49	BCL3	chr12:57852545-57853684	A549	lung:	n/a	n/a
50	SIN3AK20	chr12:57853398-57853564	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:57853396-57853446	IMR90	lung:	fetal
2	chr12:57853396-57853446	RPTEC	kidney:	n/a
3	chr12:57853396-57853446	Jurkat	blood:	n/a
4	chr12:57853396-57853446	HCT-116	colon:	n/a
5	chr12:57853396-57853446	GM12892	blood:	n/a
6	chr12:57853396-57853446	GM06990	blood:	n/a
7	chr12:57853396-57853446	NHDF-neo	bronchial:	n/a
8	chr12:57853396-57853446	SK-N-MC	brain:	n/a
9	chr12:57853396-57853446	NT2-D1	testis:	n/a
10	chr12:57853396-57853446	HAEpiC	amniotic membrane:	n/a
11	chr12:57853396-57853446	H1-hESC	embryonic stem cell:	embryo
12	chr12:57853396-57853446	LNCaP	prostate:	n/a
13	chr12:57853396-57853446	ovcar-3	ovarian:	n/a
14	chr12:57853396-57853446	U87	brain:	n/a
15	chr12:57853396-57853446	NH-A	brain:	n/a
16	chr12:57853396-57853446	K562	blood:	n/a
17	chr12:57853396-57853446	CMK	blood:	n/a
18	chr12:57853396-57853446	ECC-1	luminal epithelium:	n/a
19	chr12:57853396-57853446	GM19239	blood:	n/a
20	chr12:57853396-57853446	HMEC	breast:	n/a
21	chr12:57853396-57853446	AG09319	gingival:	n/a
22	chr12:57853396-57853446	SAEC	small airway:	n/a
23	chr12:57853396-57853446	MCF10A-Er-Src	breast:	n/a
24	chr12:57853396-57853446	NB4	blood:	n/a
25	chr12:57853396-57853446	HL-60	blood:	n/a
26	chr12:57853396-57853446	HRE	kidney:	n/a
27	chr12:57853396-57853446	AG09309	skin:	n/a
28	chr12:57853396-57853446	HEK293	kidney:	embryo
29	chr12:57853396-57853446	GM12891	blood:	n/a
30	chr12:57853396-57853446	PFSK-1	brain:	n/a
31	chr12:57853396-57853446	HPAEpiC	pulmonary alveolar:	n/a
32	chr12:57853396-57853446	AG10803	skin:	n/a
33	chr12:57853396-57853446	HRCEpiC	kidney:	n/a
34	chr12:57853396-57853446	HEEpiC	esophagus:	n/a
35	chr12:57853396-57853446	Hela-S3	cervix:	n/a
36	chr12:57853396-57853446	BE2_C	brain:	n/a
37	chr12:57853396-57853446	HCF	heart:	n/a
38	chr12:57853396-57853446	HCPEpiC	choroid plexus:	n/a
39	chr12:57853396-57853446	HIPEpiC	eye:	n/a
40	chr12:57853396-57853446	A549	lung:	n/a
41	chr12:57853396-57853446	SKMC	muscle:	n/a
42	chr12:57853396-57853446	HNPCEpiC	eye:	n/a
43	chr12:57853396-57853446	PANC-1	pancreas:	n/a
44	chr12:57853396-57853446	BJ	skin:	n/a
45	chr12:57853396-57853446	NHBE	bronchial:	n/a
46	chr12:57853396-57853446	Hepatocyte	liver:	n/a
47	chr12:57853396-57853446	HRPEpiC	eye:	n/a
48	chr12:57853396-57853446	T-47D	breast:	n/a
49	chr12:57853396-57853446	Caco-2	colon:	n/a
50	chr12:57853396-57853446	ProgFib	skin:	n/a

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	chr12:57849885..57859254-chr12:57908711..57915821,16	K562	blood:
5	chr12:57822750..57826133-chr12:57852904..57855936,4	K562	blood:
6	chr12:57693773..57695685-chr12:57852034..57854514,2	K562	blood:
7	chr12:57852034..57858739-chr12:57911478..57917144,8	MCF-7	breast:
8	chr12:57633619..57639143-chr12:57853203..57857806,7	K562	blood:
9	chr12:57852892..57855767-chr12:58158814..58160402,2	K562	blood:
10	chr12:57851728..57854572-chr12:58144859..58146430,2	MCF-7	breast:
11	chr12:57820715..57827591-chr12:57847165..57857509,18	K562	blood:
12	chr12:57848876..57851404-chr12:57851445..57853731,2	MCF-7	breast:
13	chr12:57850154..57858218-chr12:57910899..57919538,20	K562	blood:

Variant related genes	Relation type
GLI1	TF binding region
GLI1	CpG island
ENSG00000175197	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000182199	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000258001	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	chr12:57852400-57853600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
2	chr12:57852400-57853600	Flanking Active TSS	Dnd41	blood
3	chr12:57852400-57853600	Flanking Active TSS	HUVEC	blood vessel
4	chr12:57852400-57853800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr12:57852400-57853800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr12:57852400-57853800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:57852400-57853800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:57852400-57854600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr12:57852400-57856600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:57852400-57856800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr12:57852600-57853800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:57852600-57853800	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr12:57852600-57854200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr12:57852600-57854200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:57852600-57854600	Active TSS	Psoas Muscle	Psoas
16	chr12:57852600-57856600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr12:57852600-57856600	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr12:57852800-57853600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:57852800-57853800	Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr12:57852800-57853800	Active TSS	Esophagus	oesophagus
21	chr12:57852800-57853800	Active TSS	Lung	lung
22	chr12:57852800-57853800	Active TSS	Placenta Amnion	Placenta Amnion
23	chr12:57852800-57853800	Active TSS	Spleen	Spleen
24	chr12:57852800-57853800	Active TSS	NHDF-Ad	bronchial
25	chr12:57852800-57854000	Active TSS	Primary monocytes fromperipheralblood	blood
26	chr12:57852800-57854000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:57852800-57854000	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr12:57852800-57854000	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr12:57852800-57854200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:57852800-57854200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:57852800-57854200	Active TSS	Primary T cells from cord blood	blood
32	chr12:57852800-57854200	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr12:57852800-57854400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr12:57852800-57854400	Active TSS	Ovary	ovary
35	chr12:57852800-57854400	Active TSS	Small Intestine	intestine
36	chr12:57852800-57854600	Active TSS	Left Ventricle	heart
37	chr12:57852800-57854800	Active TSS	Right Atrium	heart
38	chr12:57852800-57856400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr12:57852800-57856600	Active TSS	H1 Cell Line	embryonic stem cell
40	chr12:57852800-57856600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:57852800-57856600	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:57852800-57856600	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr12:57852800-57856600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:57852800-57856600	Active TSS	Aorta	Aorta
45	chr12:57853000-57853600	Active TSS	Fetal Brain Male	brain
46	chr12:57853000-57853800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:57853000-57853800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:57853000-57853800	Active TSS	Placenta	Placenta
49	chr12:57853000-57853800	Active TSS	Gastric	stomach
50	chr12:57853000-57853800	Active TSS	Pancreas	Pancrea

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