Variant report

Variant	rs17554139
Chromosome Location	chr12:120554632-120554633
allele	A/C/G/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	REST	chr12:120554542-120555041	PFSK-1	brain:	n/a	n/a
2	YY1	chr12:120554401-120554938	GM12891	blood:	n/a	chr12:120554587-120554598 chr12:120554748-120554762
3	POLR2A	chr12:120554321-120555298	Gliobla	brain:	n/a	n/a
4	RUNX3	chr12:120554408-120555625	GM12878	blood:	n/a	n/a
5	RCOR1	chr12:120554495-120555035	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:120554368-120555710	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:120554023-120555023	K562	blood:	n/a	n/a
8	E2F4	chr12:120554463-120554929	K562	blood:	n/a	chr12:120554614-120554624 chr12:120554589-120554598 chr12:120554611-120554621 chr12:120554726-120554735 chr12:120554663-120554672 chr12:120554640-120554652
9	BCL3	chr12:120554476-120555547	A549	lung:	n/a	chr12:120555156-120555169 chr12:120554609-120554622 chr12:120554525-120554538 chr12:120555031-120555040 chr12:120554615-120554624 chr12:120554586-120554595
10	POLR2A	chr12:120554296-120555415	A549	lung:	n/a	n/a
11	MTA3	chr12:120554310-120555833	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:120554393-120554947	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr12:120553643-120555735	A549	lung:	n/a	chr12:120554993-120555003
14	ELK1	chr12:120554506-120554961	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:120554330-120555034	U87	brain:	n/a	n/a
16	MAX	chr12:120554466-120555616	H1-hESC	embryonic stem cell:	n/a	chr12:120554993-120555003
17	POLR2A	chr12:120554030-120555603	GM18951	blood:	n/a	n/a
18	IRF1	chr12:120554476-120555426	K562	blood:	n/a	chr12:120554959-120554973 chr12:120554644-120554658 chr12:120554544-120554553
19	JUND	chr12:120553964-120555329	A549	lung:	n/a	chr12:120555121-120555130 chr12:120554644-120554653
20	PML	chr12:120554363-120555052	K562	blood:	n/a	n/a
21	POLR2A	chr12:120554487-120554989	HCT-116	colon:	n/a	n/a
22	YY1	chr12:120554567-120555066	A549	lung:	n/a	chr12:120554996-120555010 chr12:120554587-120554598 chr12:120554748-120554762
23	MAX	chr12:120554415-120555119	K562	blood:	n/a	chr12:120554993-120555003
24	GTF2F1	chr12:120554552-120554921	K562	blood:	n/a	n/a
25	MXI1	chr12:120554481-120555649	Hela-S3	cervix:	n/a	chr12:120555481-120555490
26	MYC	chr12:120554498-120555557	K562	blood:	n/a	chr12:120554993-120555003
27	POLR2A	chr12:120553814-120555709	HepG2	liver:	n/a	n/a
28	POLR2A	chr12:120554014-120555264	K562	blood:	n/a	n/a
29	CEBPD	chr12:120554430-120555001	HepG2	liver:	n/a	n/a
30	YY1	chr12:120554448-120554909	HCT-116	colon:	n/a	chr12:120554587-120554598 chr12:120554748-120554762
31	GABPA	chr12:120554333-120555205	A549	lung:	n/a	chr12:120554662-120554673 chr12:120554725-120554736 chr12:120554690-120554704 chr12:120554662-120554676 chr12:120554725-120554739 chr12:120554659-120554673 chr12:120554725-120554734 chr12:120554662-120554671
32	POLR2A	chr12:120554347-120555307	SK-N-SH	brain:	n/a	n/a
33	YY1	chr12:120554314-120554956	K562	blood:	n/a	chr12:120554587-120554598 chr12:120554748-120554762
34	TAF1	chr12:120554468-120554890	GM12892	blood:	n/a	n/a
35	ATF3	chr12:120554445-120554874	K562	blood:	n/a	chr12:120554711-120554720
36	POLR2A	chr12:120554301-120555534	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr12:120554361-120555024	GM12892	blood:	n/a	n/a
38	ZNF263	chr12:120554448-120555017	HEK293-T-REx	kidney:	n/a	chr12:120554623-120554644 chr12:120554597-120554606 chr12:120554637-120554646 chr12:120554600-120554609 chr12:120554583-120554604
39	SP1	chr12:120554404-120555214	A549	lung:	n/a	chr12:120555044-120555053 chr12:120555044-120555053 chr12:120554647-120554657 chr12:120555044-120555054 chr12:120554646-120554658 chr12:120554959-120554971 chr12:120554647-120554656 chr12:120555065-120555074 chr12:120554960-120554969 chr12:120554959-120554971 chr12:120554960-120554970 chr12:120555063-120555075 chr12:120554594-120554608 chr12:120554961-120554970 chr12:120555045-120555054 chr12:120555063-120555075 chr12:120555043-120555055 chr12:120554646-120554658 chr12:120554648-120554657 chr12:120554961-120554970 chr12:120554995-120555009 chr12:120555044-120555058 chr12:120555043-120555055 chr12:120554647-120554656 chr12:120555064-120555074
40	MAZ	chr12:120554422-120555430	Hela-S3	cervix:	n/a	chr12:120554993-120555003
41	CREB1	chr12:120554409-120555042	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr12:120554475-120555193	HL-60	blood:	n/a	n/a
43	HCFC1	chr12:120554474-120555059	K562	blood:	n/a	n/a
44	POLR2A	chr12:120554347-120555545	U87	brain:	n/a	n/a
45	PAX5	chr12:120554299-120555163	GM12892	blood:	n/a	chr12:120554726-120554735 chr12:120554932-120554941
46	EGR1	chr12:120554289-120554828	K562	blood:	n/a	chr12:120554663-120554672 chr12:120554726-120554735 chr12:120554725-120554734 chr12:120554458-120554472
47	SMC3	chr12:120554506-120554939	Hela-S3	cervix:	n/a	n/a
48	TAF1	chr12:120554323-120554983	K562	blood:	n/a	n/a
49	PML	chr12:120554425-120554980	K562	blood:	n/a	n/a
50	FOXP2	chr12:120554418-120554949	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120552974..120555854-chr12:120934971..120936620,2	K562	blood:
2	chr12:120537048..120541245-chr12:120553607..120557723,6	MCF-7	breast:
3	chr12:120552488..120558210-chr12:120630092..120634088,8	MCF-7	breast:
4	chr12:120553857..120555514-chr12:120592469..120594964,2	MCF-7	breast:
5	chr12:120551826..120556882-chr12:120630846..120640383,26	K562	blood:
6	chr12:120554464..120555422-chr13:37574233..37574748,2	NB4	blood:
7	chr12:120548888..120559202-chr12:120724492..120734002,35	MCF-7	breast:
8	chr12:120554154..120554853-chr15:75493750..75494389,2	MCF-7	breast:
9	chr12:120553957..120557976-chr12:120571615..120578270,6	MCF-7	breast:
10	chr12:120534104..120540073-chr12:120552292..120555790,7	K562	blood:
11	chr12:120516359..120519600-chr12:120552938..120556302,7	MCF-7	breast:
12	chr12:120553299..120556376-chr12:120632430..120634315,3	MCF-7	breast:
13	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
14	chr1:161039605..161040134-chr12:120554428..120555097,2	NB4	blood:
15	chr12:120554072..120556853-chr12:120607712..120610177,2	K562	blood:
16	chr12:120553041..120557313-chr12:120636619..120640383,10	K562	blood:
17	chr12:120528996..120531217-chr12:120552975..120554934,2	MCF-7	breast:
18	chr12:120551105..120556435-chr12:120727138..120732848,13	K562	blood:
19	chr12:120552161..120556177-chr12:120630368..120635589,11	K562	blood:
20	chr12:120425209..120429306-chr12:120552934..120555400,5	MCF-7	breast:
21	chr12:120551667..120557354-chr12:120726466..120731431,13	MCF-7	breast:
22	chr12:120552903..120558662-chr12:120635855..120639972,12	MCF-7	breast:
23	chr12:120551112..120557922-chr12:120727181..120731830,12	K562	blood:
24	chr12:120553785..120557408-chr12:120702135..120705915,4	K562	blood:
25	chr12:120554030..120557390-chr12:120602676..120607116,4	MCF-7	breast:

Variant related genes	Relation type
RAB35	TF binding region
ENSG00000186517	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000266704	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000120699	Chromatin interaction
ENSG00000088986	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000120697	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000089154	Chromatin interaction
ENSG00000263913	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	esv3408817	chr12:120553094-120555942	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv3345428	chr12:120553419-120556067	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 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	chr12:120553400-120555800	Active TSS	Aorta	Aorta
2	chr12:120553400-120556000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:120553600-120555600	Active TSS	Fetal Muscle Trunk	muscle
4	chr12:120553600-120555600	Active TSS	Gastric	stomach
5	chr12:120553600-120555800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:120553600-120555800	Active TSS	Ovary	ovary
7	chr12:120553600-120556000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr12:120553600-120556000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr12:120553600-120556200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:120553600-120556200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:120553600-120556200	Active TSS	Esophagus	oesophagus
12	chr12:120553600-120556200	Active TSS	Lung	lung
13	chr12:120553600-120556200	Active TSS	GM12878-XiMat	blood
14	chr12:120553600-120556200	Active TSS	NHLF	lung
15	chr12:120553600-120556600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:120553800-120554800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:120553800-120555600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:120553800-120555800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:120553800-120555800	Active TSS	Left Ventricle	heart
20	chr12:120553800-120556000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:120553800-120556000	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr12:120553800-120556000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr12:120553800-120556000	Active TSS	Small Intestine	intestine
24	chr12:120553800-120556000	Active TSS	NHDF-Ad	bronchial
25	chr12:120553800-120556200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:120553800-120556200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:120553800-120556200	Active TSS	Psoas Muscle	Psoas
28	chr12:120553800-120556200	Active TSS	Right Ventricle	heart
29	chr12:120553800-120556400	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:120553800-120556400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:120553800-120556400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:120553800-120556800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr12:120554000-120554800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:120554000-120555200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:120554000-120555200	Active TSS	Fetal Stomach	stomach
36	chr12:120554000-120555400	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr12:120554000-120555400	Active TSS	Brain Germinal Matrix	brain
38	chr12:120554000-120555400	Active TSS	Brain Substantia Nigra	brain
39	chr12:120554000-120555400	Active TSS	Duodenum Mucosa	Duodenum
40	chr12:120554000-120555400	Active TSS	Fetal Brain Male	brain
41	chr12:120554000-120555400	Active TSS	Fetal Brain Female	brain
42	chr12:120554000-120555400	Active TSS	Rectal Smooth Muscle	rectum
43	chr12:120554000-120555400	Active TSS	HUVEC	blood vessel
44	chr12:120554000-120555400	Active TSS	Osteobl	bone
45	chr12:120554000-120555600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:120554000-120555600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:120554000-120555600	Active TSS	Brain Anterior Caudate	brain
48	chr12:120554000-120555600	Active TSS	Colon Smooth Muscle	Colon
49	chr12:120554000-120555600	Active TSS	Fetal Intestine Small	intestine
50	chr12:120554000-120555600	Active TSS	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links