Variant report

Variant	rs538552421
Chromosome Location	chr12:49454814-49454815
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	PRDM1	chr12:49454776-49455185	Hela-S3	cervix:	n/a	chr12:49454926-49454941
2	NFATC1	chr12:49454385-49454888	GM12878	blood:	n/a	n/a
3	RUNX3	chr12:49453962-49455109	GM12878	blood:	n/a	n/a
4	WRNIP1	chr12:49454442-49455198	GM12878	blood:	n/a	n/a
5	MAX	chr12:49453904-49455216	HepG2	liver:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
6	GABPA	chr12:49453998-49454958	A549	lung:	n/a	chr12:49454180-49454189
7	TEAD4	chr12:49454360-49454840	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr12:49454120-49455138	K562	blood:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
9	FOXM1	chr12:49454059-49454997	GM12878	blood:	n/a	n/a
10	ELF1	chr12:49454217-49454821	A549	lung:	n/a	chr12:49454278-49454290
11	POLR2A	chr12:49453908-49454860	A549	lung:	n/a	n/a
12	POLR2A	chr12:49453789-49455394	K562	blood:	n/a	n/a
13	ATF2	chr12:49454115-49454827	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:49453535-49455032	H1-hESC	embryonic stem cell:	n/a	n/a
15	CHD1	chr12:49451619-49455170	IMR90	lung:	n/a	chr12:49454043-49454053 chr12:49454374-49454384 chr12:49453842-49453852
16	POLR2A	chr12:49453593-49454906	GM10847	blood:	n/a	n/a
17	MAX	chr12:49453645-49455144	HepG2	liver:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
18	POLR2A	chr12:49452782-49455199	HUVEC	blood vessel:	n/a	n/a
19	TCF12	chr12:49453918-49455260	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr12:49453533-49455168	HUVEC	blood vessel:	n/a	n/a
21	BHLHE40	chr12:49454419-49454861	HepG2	liver:	n/a	chr12:49454670-49454686
22	E2F6	chr12:49454528-49454845	K562	blood:	n/a	chr12:49454757-49454766
23	POLR2A	chr12:49453984-49455101	GM12878	blood:	n/a	n/a
24	RXRA	chr12:49454347-49454833	GM12878	blood:	n/a	chr12:49454588-49454595
25	E2F6	chr12:49454472-49454855	K562	blood:	n/a	chr12:49454757-49454766
26	NFIC	chr12:49454035-49455003	ECC-1	luminal epithelium:	n/a	n/a
27	MYC	chr12:49454150-49455080	Hela-S3	cervix:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
28	TAF1	chr12:49454015-49455082	K562	blood:	n/a	n/a
29	MAX	chr12:49453436-49455228	ECC-1	luminal epithelium:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49453616-49453625 chr12:49454690-49454701
30	POLR2A	chr12:49453033-49455284	Hela-S3	cervix:	n/a	n/a
31	BCL3	chr12:49454053-49455212	A549	lung:	n/a	chr12:49454720-49454729 chr12:49454357-49454370 chr12:49454950-49454963 chr12:49454180-49454193 chr12:49454892-49454905 chr12:49454573-49454582 chr12:49454363-49454376
32	E2F4	chr12:49454425-49454927	MCF10A-Er-Src	breast:	n/a	chr12:49454757-49454766
33	POLR2A	chr12:49453637-49455095	MCF-7	breast:	n/a	n/a
34	TBL1XR1	chr12:49454438-49455106	K562	blood:	n/a	n/a
35	EP300	chr12:49454345-49455004	GM12878	blood:	n/a	chr12:49454713-49454729
36	CHD2	chr12:49454272-49454944	H1-hESC	embryonic stem cell:	n/a	chr12:49454374-49454384
37	MYC	chr12:49454407-49454902	H1-hESC	embryonic stem cell:	n/a	chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
38	ZC3H11A	chr12:49454420-49454903	K562	blood:	n/a	n/a
39	ZNF143	chr12:49454228-49455097	K562	blood:	n/a	chr12:49454271-49454289 chr12:49454899-49454918 chr12:49454370-49454388 chr12:49454904-49454922
40	ATF2	chr12:49454229-49454848	GM12878	blood:	n/a	n/a
41	HDAC2	chr12:49454134-49455204	MCF-7	breast:	n/a	n/a
42	MAX	chr12:49454441-49454944	H1-hESC	embryonic stem cell:	n/a	chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
43	CEBPD	chr12:49454507-49454824	HepG2	liver:	n/a	n/a
44	ZBTB7A	chr12:49453691-49455037	K562	blood:	n/a	chr12:49454089-49454096
45	MTA3	chr12:49452741-49455410	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:49453336-49455117	GM18951	blood:	n/a	n/a
47	MAFK	chr12:49454427-49455089	Hela-S3	cervix:	n/a	n/a
48	MAFK	chr12:49454300-49455057	K562	blood:	n/a	n/a
49	ATF2	chr12:49454237-49455154	H1-hESC	embryonic stem cell:	n/a	n/a
50	SIX5	chr12:49454447-49455093	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:49454806-49454856	RPTEC	kidney:	n/a
2	chr12:49454806-49454856	U87	brain:	n/a
3	chr12:49454806-49454856	NHDF-neo	bronchial:	n/a
4	chr12:49454806-49454856	HEK293	kidney:	embryo
5	chr12:49454806-49454856	NT2-D1	testis:	n/a
6	chr12:49454806-49454856	MCF10A-Er-Src	breast:	n/a
7	chr12:49454806-49454856	CMK	blood:	n/a
8	chr12:49454806-49454856	HEEpiC	esophagus:	n/a
9	chr12:49454806-49454856	GM12891	blood:	n/a
10	chr12:49454806-49454856	HCF	heart:	n/a
11	chr12:49454806-49454856	HNPCEpiC	eye:	n/a
12	chr12:49454806-49454856	SK-N-MC	brain:	n/a
13	chr12:49454806-49454856	GM12878	blood:	n/a
14	chr12:49454806-49454856	IMR90	lung:	fetal
15	chr12:49454806-49454856	T-47D	breast:	n/a
16	chr12:49454806-49454856	GM06990	blood:	n/a
17	chr12:49454806-49454856	Hela-S3	cervix:	n/a
18	chr12:49454806-49454856	SK-N-SH	brain:	n/a
19	chr12:49454806-49454856	Caco-2	colon:	n/a
20	chr12:49454806-49454856	HepG2	liver:	n/a
21	chr12:49454806-49454856	HRPEpiC	eye:	n/a
22	chr12:49454806-49454856	HCM	heart:	n/a
23	chr12:49454806-49454856	Hepatocyte	liver:	n/a
24	chr12:49454806-49454856	A549	lung:	n/a
25	chr12:49454806-49454856	AG10803	skin:	n/a
26	chr12:49454806-49454856	K562	blood:	n/a
27	chr12:49454806-49454856	H1-hESC	embryonic stem cell:	embryo
28	chr12:49454806-49454856	MCF-7	breast:	n/a
29	chr12:49454806-49454856	HIPEpiC	eye:	n/a
30	chr12:49454806-49454856	AoSMC	blood vessel:	n/a
31	chr12:49454806-49454856	GM19239	blood:	n/a
32	chr12:49454806-49454856	AG09309	skin:	n/a
33	chr12:49454806-49454856	ECC-1	luminal epithelium:	n/a
34	chr12:49454806-49454856	Jurkat	blood:	n/a
35	chr12:49454806-49454856	HMEC	breast:	n/a
36	chr12:49454806-49454856	AG09319	gingival:	n/a
37	chr12:49454806-49454856	NHBE	bronchial:	n/a
38	chr12:49454806-49454856	SK-N-SH_RA	brain:	n/a
39	chr12:49454806-49454856	ovcar-3	ovarian:	n/a
40	chr12:49454806-49454856	AG04449	skin:	fetal
41	chr12:49454806-49454856	NB4	blood:	n/a
42	chr12:49454806-49454856	HPAEpiC	pulmonary alveolar:	n/a
43	chr12:49454806-49454856	HUVEC	blood vessel:	n/a
44	chr12:49454806-49454856	GM12892	blood:	n/a
45	chr12:49454806-49454856	HRE	kidney:	n/a
46	chr12:49454806-49454856	PrEC	prostate:	n/a
47	chr12:49454806-49454856	ProgFib	skin:	n/a
48	chr12:49454806-49454856	SKMC	muscle:	n/a
49	chr12:49454806-49454856	NH-A	brain:	n/a
50	chr12:49454806-49454856	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr12:49447251..49459518-chr12:49480338..49487981,17	K562	blood:
2	chr12:49446392..49469923-chr12:49518127..49527853,66	K562	blood:
3	chr12:49454044..49455042-chr7:74489029..74489605,2	Hela-S3	cervix:
4	chr12:49454563..49455155-chr7:87848985..87849619,2	Hela-S3	cervix:
5	chr12:49452282..49457106-chr12:49501761..49505806,6	K562	blood:
6	chr12:49454519..49456146-chr12:49518450..49520745,2	MCF-7	breast:
7	chr12:49408338..49419708-chr12:49447252..49460551,38	K562	blood:
8	chr12:49453309..49455961-chr12:49948897..49951747,2	MCF-7	breast:
9	chr1:144534155..144534667-chr12:49454018..49454864,2	Hela-S3	cervix:
10	chr12:49453115..49455291-chr12:49657846..49660975,4	MCF-7	breast:
11	chr12:49454021..49456179-chr12:49508366..49510938,2	K562	blood:
12	chr12:49452588..49458658-chr12:49486666..49491439,6	MCF-7	breast:
13	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
14	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
15	chr12:49454631..49456849-chr12:49504734..49506537,2	K562	blood:
16	chr12:49454377..49456128-chr12:49555146..49557266,2	K562	blood:
17	chr12:49409714..49416851-chr12:49447402..49455499,24	MCF-7	breast:
18	chr12:49450455..49459531-chr12:49522374..49527837,16	MCF-7	breast:
19	chr12:49454627..49456339-chr12:49470882..49473684,2	K562	blood:
20	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
21	chr12:49449329..49454848-chr12:49480302..49484566,6	K562	blood:
22	chr12:49365267..49367565-chr12:49453514..49456197,2	K562	blood:
23	chr12:49454177..49455905-chr12:49464920..49466529,2	MCF-7	breast:
24	chr12:49453076..49457977-chr12:49485062..49491403,12	K562	blood:
25	chr12:46765603..46767339-chr12:49452531..49455344,2	K562	blood:
26	chr12:49450480..49457103-chr12:49487982..49492074,8	K562	blood:
27	chr12:49453688..49456279-chr12:49494326..49496673,3	K562	blood:
28	chr12:49454318..49454923-chr6:26033379..26034226,2	Hela-S3	cervix:
29	chr12:49453979..49454864-chr5:82372935..82373905,2	Hela-S3	cervix:
30	chr12:49418054..49419744-chr12:49454256..49456208,2	MCF-7	breast:
31	chr12:49452850..49457008-chr12:49658832..49661007,5	MCF-7	breast:
32	chr10:14920093..14920668-chr12:49454106..49455063,2	Hela-S3	cervix:
33	chr12:49211350..49214001-chr12:49453993..49456972,2	MCF-7	breast:
34	chr12:49432703..49444457-chr12:49447982..49454860,15	MCF-7	breast:
35	chr12:49407466..49416688-chr12:49451532..49456163,12	MCF-7	breast:
36	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
37	chr12:49453099..49454977-chr16:2313964..2316664,2	MCF-7	breast:

Variant related genes	Relation type
KMT2D	TF binding region
KMT2D	CpG island
ENSG00000137259	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000075142	Chromatin interaction
ENSG00000205937	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000174695	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000152422	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000139636	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
6	esv3360842	chr12:49452910-49455458	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49450200-49455200	Active TSS	HSMMtube	muscle
2	chr12:49450800-49455400	Active TSS	Fetal Kidney	kidney
3	chr12:49451200-49455200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:49451400-49455200	Active TSS	Lung	lung
5	chr12:49451800-49455000	Active TSS	Muscle Satellite Cultured Cells	--
6	chr12:49451800-49455000	Active TSS	GM12878-XiMat	blood
7	chr12:49451800-49455200	Active TSS	HSMM	muscle
8	chr12:49451800-49455600	Active TSS	NHDF-Ad	bronchial
9	chr12:49452000-49455000	Active TSS	Fetal Intestine Small	intestine
10	chr12:49452000-49455200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:49452000-49455200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:49452000-49455200	Active TSS	Psoas Muscle	Psoas
13	chr12:49452000-49455200	Bivalent/Poised TSS	HepG2	liver
14	chr12:49452000-49455400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:49452000-49455400	Active TSS	Esophagus	oesophagus
16	chr12:49452200-49455400	Active TSS	Aorta	Aorta
17	chr12:49452400-49455000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:49452400-49455200	Active TSS	Gastric	stomach
19	chr12:49452400-49455200	Active TSS	Small Intestine	intestine
20	chr12:49452400-49455200	Active TSS	A549	lung
21	chr12:49452400-49455400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:49452400-49455400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr12:49452400-49455400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:49452400-49455600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:49452600-49455000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:49452600-49455000	Active TSS	Fetal Heart	heart
27	chr12:49452600-49455000	Active TSS	Fetal Intestine Large	intestine
28	chr12:49452600-49455000	Active TSS	Pancreas	Pancrea
29	chr12:49452600-49455000	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr12:49452600-49455200	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:49452600-49455400	Active TSS	Rectal Smooth Muscle	rectum
32	chr12:49452600-49455400	Active TSS	HMEC	breast
33	chr12:49452800-49455000	Active TSS	NHEK	skin
34	chr12:49452800-49455200	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr12:49452800-49455200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:49452800-49455200	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr12:49452800-49455200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:49452800-49455200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:49452800-49455200	Active TSS	Ovary	ovary
40	chr12:49452800-49455400	Active TSS	Colon Smooth Muscle	Colon
41	chr12:49452800-49455400	Active TSS	Left Ventricle	heart
42	chr12:49452800-49455400	Active TSS	Hela-S3	cervix
43	chr12:49452800-49455400	Active TSS	NHLF	lung
44	chr12:49452800-49455600	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr12:49453000-49455000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:49453000-49455000	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr12:49453000-49455000	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr12:49453000-49455000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:49453000-49455000	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr12:49453000-49455000	Active TSS	Fetal Lung	lung

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