Variant report

Variant	rs567028839
Chromosome Location	chr12:49453692-49453693
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	POLR2A	chr12:49453535-49455032	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD1	chr12:49451619-49455170	IMR90	lung:	n/a	chr12:49454043-49454053 chr12:49454374-49454384 chr12:49453842-49453852
3	POLR2A	chr12:49453593-49454906	GM10847	blood:	n/a	n/a
4	MAX	chr12:49453645-49455144	HepG2	liver:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49454690-49454701
5	POLR2A	chr12:49452782-49455199	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr12:49453533-49455168	HUVEC	blood vessel:	n/a	n/a
7	UBTF	chr12:49452969-49454790	K562	blood:	n/a	n/a
8	TCF12	chr12:49452603-49453813	A549	lung:	n/a	n/a
9	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
10	POLR2A	chr12:49453033-49455284	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:49453637-49455095	MCF-7	breast:	n/a	n/a
12	GABPA	chr12:49453580-49453942	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZBTB7A	chr12:49453691-49455037	K562	blood:	n/a	chr12:49454089-49454096
14	MTA3	chr12:49452741-49455410	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:49453336-49455117	GM18951	blood:	n/a	n/a
16	TAF1	chr12:49453677-49454937	HepG2	liver:	n/a	n/a
17	TEAD4	chr12:49453602-49454888	ECC-1	luminal epithelium:	n/a	n/a
18	JUND	chr12:49453566-49455155	A549	lung:	n/a	chr12:49454115-49454124 chr12:49453840-49453849
19	ELF1	chr12:49453481-49455109	GM12878	blood:	n/a	chr12:49454278-49454290
20	POLR2A	chr12:49453586-49455210	GM12891	blood:	n/a	n/a
21	TCF12	chr12:49453092-49455328	ECC-1	luminal epithelium:	n/a	n/a
22	MAZ	chr12:49452677-49455391	IMR90	lung:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49453616-49453625 chr12:49454690-49454701
23	POLR2A	chr12:49452959-49455403	K562	blood:	n/a	n/a
24	CTCF	chr12:49453640-49453790	GM12874	blood:	n/a	n/a
25	POLR2A	chr12:49453592-49455093	A549	lung:	n/a	n/a
26	HEY1	chr12:49453629-49453855	HepG2	liver:	n/a	chr12:49453835-49453850
27	TAF1	chr12:49453319-49455161	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr12:49453127-49455315	Hela-S3	cervix:	n/a	n/a
29	CHD2	chr12:49453587-49455138	Hela-S3	cervix:	n/a	chr12:49454043-49454053 chr12:49454374-49454384 chr12:49453842-49453852
30	POLR2A	chr12:49453615-49455116	ECC-1	luminal epithelium:	n/a	n/a
31	SIN3A	chr12:49453141-49455163	H1-hESC	embryonic stem cell:	n/a	chr12:49454951-49454960 chr12:49453619-49453629 chr12:49453369-49453382 chr12:49453620-49453633
32	ZNF143	chr12:49453617-49453764	H1-hESC	embryonic stem cell:	n/a	n/a
33	TCF7L2	chr12:49453000-49454932	Hela-S3	cervix:	n/a	chr12:49453675-49453685 chr12:49453671-49453687 chr12:49453672-49453686 chr12:49453671-49453687 chr12:49453672-49453686 chr12:49453675-49453684
34	CREB1	chr12:49453382-49453816	A549	lung:	n/a	n/a
35	ELF1	chr12:49453612-49453946	K562	blood:	n/a	n/a
36	POLR2A	chr12:49453576-49454899	IMR90	lung:	n/a	n/a
37	POLR2A	chr12:49453039-49455380	H1-hESC	embryonic stem cell:	n/a	n/a
38	YY1	chr12:49453634-49455026	K562	blood:	n/a	chr12:49453836-49453845 chr12:49454382-49454391 chr12:49454180-49454189 chr12:49454721-49454730
39	YY1	chr12:49453223-49455168	HepG2	liver:	n/a	chr12:49453836-49453845 chr12:49454382-49454391 chr12:49454180-49454189 chr12:49454721-49454730
40	TAF1	chr12:49453105-49455372	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr12:49453235-49455116	NB4	blood:	n/a	n/a
42	POLR2A	chr12:49453587-49455232	MCF-7	breast:	n/a	n/a
43	MAZ	chr12:49453481-49455222	K562	blood:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49453616-49453625 chr12:49454690-49454701
44	POLR2A	chr12:49453639-49455050	GM12892	blood:	n/a	n/a
45	POLR2A	chr12:49453588-49455103	GM19099	blood:	n/a	n/a
46	MAX	chr12:49453198-49455330	Hela-S3	cervix:	n/a	chr12:49454185-49454195 chr12:49454708-49454718 chr12:49454689-49454699 chr12:49453616-49453625 chr12:49454690-49454701
47	HCFC1	chr12:49453548-49455210	K562	blood:	n/a	n/a
48	YY1	chr12:49453496-49455130	ECC-1	luminal epithelium:	n/a	chr12:49453836-49453845 chr12:49454382-49454391 chr12:49454180-49454189 chr12:49454721-49454730
49	UBTF	chr12:49453152-49454880	K562	blood:	n/a	n/a
50	POLR2A	chr12:49453525-49455216	Raji	blood:	n/a	n/a

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	chr12:49452282..49457106-chr12:49501761..49505806,6	K562	blood:
4	chr12:49408338..49419708-chr12:49447252..49460551,38	K562	blood:
5	chr12:49453309..49455961-chr12:49948897..49951747,2	MCF-7	breast:
6	chr12:49210248..49212975-chr12:49452451..49454269,2	MCF-7	breast:
7	chr12:49453115..49455291-chr12:49657846..49660975,4	MCF-7	breast:
8	chr12:49245786..49247623-chr12:49451692..49454310,2	MCF-7	breast:
9	chr12:49452588..49458658-chr12:49486666..49491439,6	MCF-7	breast:
10	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
11	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
12	chr12:49453107..49454677-chr12:49580973..49582766,2	K562	blood:
13	chr12:49409714..49416851-chr12:49447402..49455499,24	MCF-7	breast:
14	chr12:49450455..49459531-chr12:49522374..49527837,16	MCF-7	breast:
15	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
16	chr12:49449329..49454848-chr12:49480302..49484566,6	K562	blood:
17	chr12:49365267..49367565-chr12:49453514..49456197,2	K562	blood:
18	chr12:49453076..49457977-chr12:49485062..49491403,12	K562	blood:
19	chr12:46765603..46767339-chr12:49452531..49455344,2	K562	blood:
20	chr12:49206889..49209222-chr12:49451651..49454239,2	MCF-7	breast:
21	chr12:49453587..49454404-chr12:49522959..49523795,2	Hela-S3	cervix:
22	chr12:49450480..49457103-chr12:49487982..49492074,8	K562	blood:
23	chr12:49452655..49454232-chr8:145150875..145152586,2	MCF-7	breast:
24	chr12:49453688..49456279-chr12:49494326..49496673,3	K562	blood:
25	chr12:49452850..49457008-chr12:49658832..49661007,5	MCF-7	breast:
26	chr12:49452631..49454255-chr12:49495979..49497484,2	MCF-7	breast:
27	chr12:49424813..49427751-chr12:49451760..49454466,2	MCF-7	breast:
28	chr12:49432703..49444457-chr12:49447982..49454860,15	MCF-7	breast:
29	chr12:49407466..49416688-chr12:49451532..49456163,12	MCF-7	breast:
30	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
31	chr12:49453099..49454977-chr16:2313964..2316664,2	MCF-7	breast:

Variant related genes	Relation type
KMT2D	TF binding region
ENSG00000135519	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000179091	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000167552	Chromatin interaction
ENSG00000205937	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000200309	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	chr12:49449200-49454200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr12:49449400-49453800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:49449800-49453800	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr12:49450200-49455200	Active TSS	HSMMtube	muscle
5	chr12:49450800-49455400	Active TSS	Fetal Kidney	kidney
6	chr12:49451200-49454200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:49451200-49455200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:49451400-49455200	Active TSS	Lung	lung
9	chr12:49451800-49455000	Active TSS	Muscle Satellite Cultured Cells	--
10	chr12:49451800-49455000	Active TSS	GM12878-XiMat	blood
11	chr12:49451800-49455200	Active TSS	HSMM	muscle
12	chr12:49451800-49455600	Active TSS	NHDF-Ad	bronchial
13	chr12:49452000-49455000	Active TSS	Fetal Intestine Small	intestine
14	chr12:49452000-49455200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:49452000-49455200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:49452000-49455200	Active TSS	Psoas Muscle	Psoas
17	chr12:49452000-49455200	Bivalent/Poised TSS	HepG2	liver
18	chr12:49452000-49455400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:49452000-49455400	Active TSS	Esophagus	oesophagus
20	chr12:49452200-49455400	Active TSS	Aorta	Aorta
21	chr12:49452400-49455000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:49452400-49455200	Active TSS	Gastric	stomach
23	chr12:49452400-49455200	Active TSS	Small Intestine	intestine
24	chr12:49452400-49455200	Active TSS	A549	lung
25	chr12:49452400-49455400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:49452400-49455400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr12:49452400-49455400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:49452400-49455600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:49452600-49454200	Active TSS	Right Atrium	heart
30	chr12:49452600-49455000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:49452600-49455000	Active TSS	Fetal Heart	heart
32	chr12:49452600-49455000	Active TSS	Fetal Intestine Large	intestine
33	chr12:49452600-49455000	Active TSS	Pancreas	Pancrea
34	chr12:49452600-49455000	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr12:49452600-49455200	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr12:49452600-49455400	Active TSS	Rectal Smooth Muscle	rectum
37	chr12:49452600-49455400	Active TSS	HMEC	breast
38	chr12:49452800-49454800	Active TSS	Placenta Amnion	Placenta Amnion
39	chr12:49452800-49454800	Active TSS	Thymus	Thymus
40	chr12:49452800-49455000	Active TSS	NHEK	skin
41	chr12:49452800-49455200	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr12:49452800-49455200	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr12:49452800-49455200	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr12:49452800-49455200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:49452800-49455200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:49452800-49455200	Active TSS	Ovary	ovary
47	chr12:49452800-49455400	Active TSS	Colon Smooth Muscle	Colon
48	chr12:49452800-49455400	Active TSS	Left Ventricle	heart
49	chr12:49452800-49455400	Active TSS	Hela-S3	cervix
50	chr12:49452800-49455400	Active TSS	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links