Variant report

Variant	rs116686330
Chromosome Location	chr12:56401887-56401888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr12:56401670-56402175	GM12878	blood:	n/a	n/a
2	MAX	chr12:56401587-56401894	K562	blood:	n/a	n/a
3	POLR2A	chr12:56401586-56402225	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr12:56400753-56402039	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr12:56400540-56402452	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZBTB7A	chr12:56401087-56401893	K562	blood:	n/a	chr12:56401271-56401285 chr12:56401270-56401284
7	MAX	chr12:56401521-56402058	ECC-1	luminal epithelium:	n/a	n/a
8	ZBTB7A	chr12:56400994-56402187	ECC-1	luminal epithelium:	n/a	chr12:56401271-56401285 chr12:56401270-56401284
9	REST	chr12:56400758-56402521	H1-neurons	neurons:	n/a	chr12:56401778-56401791
10	CHD1	chr12:56401718-56402099	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr12:56400685-56402279	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr12:56400647-56401957	K562	blood:	n/a	n/a
13	POLR2A	chr12:56401599-56401898	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr12:56400985-56402134	H1-neurons	neurons:	n/a	n/a
15	TAF1	chr12:56401580-56402259	H1-hESC	embryonic stem cell:	n/a	n/a
16	WRNIP1	chr12:56401804-56401960	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:56400840-56401931	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr12:56400804-56402240	H1-hESC	embryonic stem cell:	n/a	n/a
19	E2F6	chr12:56401606-56401902	K562	blood:	n/a	n/a
20	E2F6	chr12:56401689-56401908	K562	blood:	n/a	n/a
21	MAZ	chr12:56400871-56401889	K562	blood:	n/a	chr12:56401436-56401446
22	TBP	chr12:56401652-56401902	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZBTB7A	chr12:56401029-56401898	K562	blood:	n/a	chr12:56401271-56401285 chr12:56401270-56401284
24	SP4	chr12:56401590-56401981	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZBTB7A	chr12:56400937-56402199	ECC-1	luminal epithelium:	n/a	chr12:56401271-56401285 chr12:56401270-56401284
26	E2F6	chr12:56401632-56402027	H1-hESC	embryonic stem cell:	n/a	n/a
27	ZBTB7A	chr12:56401538-56401896	HepG2	liver:	n/a	n/a
28	TAF1	chr12:56401585-56401937	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:56401554-56402063	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr12:56401385-56401971	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr12:56401561-56401930	H1-hESC	embryonic stem cell:	n/a	n/a
32	SIN3A	chr12:56401650-56402067	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr12:56401531-56401943	GM12892	blood:	n/a	n/a
34	EGR1	chr12:56401455-56401890	ECC-1	luminal epithelium:	n/a	chr12:56401549-56401563 chr12:56401570-56401584 chr12:56401614-56401628 chr12:56401496-56401505
35	POLR2A	chr12:56401562-56402235	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:56400584-56402103	K562	blood:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56399175..56403137-chr12:56403716..56405667,4	MCF-7	breast:
2	chr12:56398217..56408038-chr12:56433794..56439966,15	K562	blood:
3	chr12:56364817..56368355-chr12:56399269..56402650,4	K562	blood:
4	chr12:56400102..56402586-chr12:56415416..56418384,2	MCF-7	breast:
5	chr12:56224367..56226323-chr12:56401356..56403743,2	MCF-7	breast:
6	chr12:56360672..56362289-chr12:56400535..56402399,2	MCF-7	breast:
7	chr12:56122770..56125786-chr12:56400050..56403264,3	K562	blood:
8	chr12:56400915..56403340-chr12:56510572..56513192,4	MCF-7	breast:
9	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
10	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
11	chr12:56399898..56405642-chr12:56433175..56438589,7	K562	blood:
12	chr12:56211633..56216017-chr12:56399885..56403410,4	MCF-7	breast:
13	chr12:56399605..56402732-chr12:56433705..56437280,6	MCF-7	breast:
14	chr12:56390809..56392348-chr12:56401235..56403925,2	K562	blood:
15	chr12:56400079..56406275-chr12:56406695..56413732,8	MCF-7	breast:
16	chr12:56399990..56402705-chr12:56510349..56512541,3	K562	blood:
17	chr12:56401139..56403498-chr12:56475848..56478502,3	K562	blood:
18	chr12:56222087..56223926-chr12:56400815..56402785,2	MCF-7	breast:
19	chr12:56318939..56322802-chr12:56399424..56402892,5	MCF-7	breast:
20	chr12:56323623..56326295-chr12:56400061..56402642,2	MCF-7	breast:
21	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:

No data

Variant related genes	Relation type
IKZF4	TF binding region
ENSG00000065361	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000229117	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3444965	chr12:56400510-56402733	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 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	chr12:56400600-56402000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:56400600-56402000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:56400600-56402000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr12:56400600-56402000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:56400600-56402000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr12:56400600-56402000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:56400600-56402000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr12:56400600-56402000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr12:56400600-56402000	Active TSS	Left Ventricle	heart
10	chr12:56400600-56402000	Active TSS	Pancreas	Pancrea
11	chr12:56400600-56402000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr12:56400600-56402000	Active TSS	Right Ventricle	heart
13	chr12:56400600-56402000	Active TSS	NHDF-Ad	bronchial
14	chr12:56400600-56402000	Active TSS	NHLF	lung
15	chr12:56400600-56402200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:56400600-56402200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr12:56400600-56402200	Active TSS	A549	lung
18	chr12:56400600-56402200	Active TSS	HSMM	muscle
19	chr12:56400600-56402400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr12:56400600-56402400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr12:56400600-56402400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:56400600-56402400	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr12:56400600-56402400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr12:56400600-56402400	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr12:56400600-56402400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:56400600-56402400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:56400600-56402400	Active TSS	Colon Smooth Muscle	Colon
28	chr12:56400600-56402400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr12:56400800-56402000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:56400800-56402000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:56400800-56402000	Active TSS	Fetal Heart	heart
32	chr12:56400800-56402000	Active TSS	Fetal Kidney	kidney
33	chr12:56400800-56402000	Active TSS	Fetal Lung	lung
34	chr12:56400800-56402200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:56400800-56402200	Active TSS	Psoas Muscle	Psoas
36	chr12:56400800-56402400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr12:56400800-56402400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:56400800-56402400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:56400800-56402400	Active TSS	Ovary	ovary
40	chr12:56401000-56402000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:56401000-56402000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:56401000-56402000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:56401000-56402000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:56401000-56402000	Active TSS	Placenta Amnion	Placenta Amnion
45	chr12:56401000-56402000	Active TSS	Small Intestine	intestine
46	chr12:56401000-56402200	Active TSS	Aorta	Aorta
47	chr12:56401000-56402200	Active TSS	Lung	lung
48	chr12:56401000-56402400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:56401200-56402000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:56401200-56402200	Active TSS	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links