Variant report

Variant	rs549331135
Chromosome Location	chr12:57400443-57400444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:239)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:239 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:57400380-57400530	HRPEpiC	eye:	n/a	n/a
2	MAX	chr12:57400202-57400620	GM12878	blood:	n/a	n/a
3	CTCF	chr12:57400279-57400559	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr12:57400420-57400570	HEEpiC	esophagus:	n/a	n/a
5	CTCF	chr12:57400400-57400550	GM12864	blood:	n/a	n/a
6	CTCF	chr12:57400360-57400510	GM12878	blood:	n/a	n/a
7	CTCF	chr12:57400420-57400570	GM12875	blood:	n/a	n/a
8	CTCF	chr12:57400340-57400490	GM12874	blood:	n/a	n/a
9	RAD21	chr12:57400397-57400571	IMR90	lung:	n/a	n/a
10	ELF1	chr12:57400308-57400580	K562	blood:	n/a	n/a
11	CTCF	chr12:57400380-57400530	HA-sp	spinal cord:	n/a	n/a
12	YY1	chr12:57400046-57400586	GM12891	blood:	n/a	chr12:57400216-57400227 chr12:57400216-57400225
13	CTCF	chr12:57399681-57400813	K562	blood:	n/a	chr12:57399761-57399770 chr12:57399931-57399949 chr12:57399757-57399770
14	CTCF	chr12:57400226-57400584	Lung_OC	lung:	n/a	n/a
15	CTCF	chr12:57400380-57400530	HCM	heart:	n/a	n/a
16	TAF1	chr12:57399971-57400715	ECC-1	luminal epithelium:	n/a	n/a
17	GABPA	chr12:57400038-57400450	K562	blood:	n/a	n/a
18	CTCF	chr12:57400360-57400510	HMEC	breast:	n/a	n/a
19	POLR2A	chr12:57399784-57400504	H1-neurons	neurons:	n/a	n/a
20	ZNF143	chr12:57400188-57400595	H1-hESC	embryonic stem cell:	n/a	n/a
21	EGR1	chr12:57400157-57400529	K562	blood:	n/a	chr12:57400330-57400344
22	MAZ	chr12:57400159-57400619	K562	blood:	n/a	n/a
23	CTCF	chr12:57400216-57400603	GM19238	blood:	n/a	n/a
24	MYC	chr12:57400228-57400448	K562	blood:	n/a	n/a
25	POLR2A	chr12:57400016-57400446	GM18526	blood:	n/a	n/a
26	CTCF	chr12:57400168-57400810	K562	blood:	n/a	n/a
27	CTCF	chr12:57400322-57400557	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr12:57400380-57400530	GM12866	blood:	n/a	n/a
29	POLR2A	chr12:57399757-57400520	K562	blood:	n/a	n/a
30	CTCF	chr12:57400360-57400510	AG04450	lung:	n/a	n/a
31	CTCF	chr12:57400420-57400570	SK-N-SH_RA	brain:	n/a	n/a
32	CTCFL	chr12:57400241-57400521	K562	blood:	n/a	n/a
33	CTCF	chr12:57400399-57400531	MCF-7	breast:	n/a	n/a
34	GABPA	chr12:57400115-57400555	SK-N-SH	brain:	n/a	n/a
35	CTCF	chr12:57400380-57400530	GM12871	blood:	n/a	n/a
36	CTCF	chr12:57400360-57400510	A549	lung:	n/a	n/a
37	CTCF	chr12:57400440-57400590	NHEK	skin:	n/a	n/a
38	CTCF	chr12:57400237-57400586	Fibrobl	skin:	n/a	n/a
39	CTCF	chr12:57400380-57400530	GM12872	blood:	n/a	n/a
40	CTCF	chr12:57400270-57400567	NHEK	skin:	n/a	n/a
41	CTCF	chr12:57399770-57400738	GM12878	blood:	n/a	chr12:57399931-57399949
42	RAD21	chr12:57400134-57400589	K562	blood:	n/a	n/a
43	CTCF	chr12:57400400-57400550	HCT-116	colon:	n/a	n/a
44	CTCF	chr12:57400400-57400550	HepG2	liver:	n/a	n/a
45	YY1	chr12:57399897-57400637	HepG2	liver:	n/a	chr12:57400216-57400227 chr12:57400216-57400225
46	CTCF	chr12:57400230-57400590	GM19240	blood:	n/a	n/a
47	CTCF	chr12:57400360-57400510	AG09319	gingival:	n/a	n/a
48	CTCF	chr12:57399860-57400897	K562	blood:	n/a	chr12:57399931-57399949
49	CTCF	chr12:57400360-57400510	GM12874	blood:	n/a	n/a
50	NFYA	chr12:57400319-57400556	Hela-S3	cervix:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57400427..57402065-chr12:57502881..57505557,2	MCF-7	breast:
2	chr12:57398945..57400725-chr12:57479656..57482846,3	MCF-7	breast:
3	chr12:57079674..57082070-chr12:57399337..57401813,2	MCF-7	breast:
4	chr12:57398623..57401161-chr12:57471695..57473634,2	MCF-7	breast:
5	chr12:57400251..57400827-chr12:57454532..57455160,2	MCF-7	breast:
6	chr12:57398801..57400743-chr12:57521280..57524489,3	K562	blood:
7	chr12:57393282..57404587-chr12:57480276..57487045,17	MCF-7	breast:
8	chr12:57398801..57400719-chr12:57521892..57524489,2	K562	blood:
9	chr12:57156641..57157497-chr12:57399996..57400652,4	MCF-7	breast:
10	chr12:57400299..57402687-chr12:57590687..57592398,2	MCF-7	breast:
11	chr12:57400180..57401732-chr12:57514933..57516523,2	K562	blood:
12	chr12:57400361..57402022-chr12:57481021..57483106,2	K562	blood:
13	chr12:57400260..57400857-chr17:59486758..59487383,2	MCF-7	breast:
14	chr12:57399976..57400833-chr12:57424825..57425490,2	MCF-7	breast:
15	chr12:56709311..56709830-chr12:57399980..57400910,2	MCF-7	breast:
16	chr12:57399687..57402362-chr12:57503183..57504772,2	K562	blood:
17	chr12:57143921..57145852-chr12:57400394..57401927,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZBTB39	TF binding region
ENSG00000166886	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000263832	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000166866	Chromatin interaction
ENSG00000025423	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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv559022	chr12:57394123-57410389	Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv3395929	chr12:57399110-57401658	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
6	esv3377733	chr12:57399235-57401433	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57398600-57400800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr12:57399000-57400600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:57399000-57400600	Active TSS	NHDF-Ad	bronchial
4	chr12:57399000-57400800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:57399000-57400800	Active TSS	HSMM	muscle
6	chr12:57399200-57400600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:57399200-57400600	Active TSS	Esophagus	oesophagus
8	chr12:57399200-57400600	Active TSS	Fetal Brain Female	brain
9	chr12:57399200-57400600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr12:57399200-57400600	Active TSS	Right Ventricle	heart
11	chr12:57399200-57400800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:57399200-57400800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:57399200-57400800	Active TSS	Left Ventricle	heart
14	chr12:57399200-57400800	Active TSS	Ovary	ovary
15	chr12:57399200-57400800	Active TSS	HSMMtube	muscle
16	chr12:57399200-57401000	Enhancers	Stomach Mucosa	stomach
17	chr12:57399400-57400600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:57399400-57400600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:57399400-57400600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:57399400-57400600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:57399400-57400600	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr12:57399400-57400600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:57399400-57400600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:57399400-57400600	Active TSS	Fetal Kidney	kidney
25	chr12:57399400-57400600	Active TSS	Fetal Stomach	stomach
26	chr12:57399400-57400600	Active TSS	Pancreas	Pancrea
27	chr12:57399400-57400600	Active TSS	Psoas Muscle	Psoas
28	chr12:57399400-57400600	Active TSS	Right Atrium	heart
29	chr12:57399400-57400600	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr12:57399400-57400600	Active TSS	A549	lung
31	chr12:57399400-57400600	Active TSS	GM12878-XiMat	blood
32	chr12:57399400-57400600	Active TSS	NHLF	lung
33	chr12:57399400-57400800	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr12:57399400-57400800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr12:57399400-57401000	Active TSS	Brain Hippocampus Middle	brain
36	chr12:57399400-57401400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:57399600-57400600	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr12:57399600-57400600	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr12:57399600-57400600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:57399600-57400600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:57399600-57400600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:57399600-57400600	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr12:57399600-57400600	Active TSS	Aorta	Aorta
44	chr12:57399600-57400600	Active TSS	Brain Germinal Matrix	brain
45	chr12:57399600-57400600	Active TSS	Brain Substantia Nigra	brain
46	chr12:57399600-57400600	Active TSS	Fetal Lung	lung
47	chr12:57399600-57400600	Active TSS	Gastric	stomach
48	chr12:57399600-57400600	Active TSS	Hela-S3	cervix
49	chr12:57399600-57400600	Active TSS	Osteobl	bone
50	chr12:57399600-57400800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links