Variant report

Variant	rs188604410
Chromosome Location	chr12:56582680-56582681
allele	A/T
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:32)
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	UBTF	chr12:56582629-56582732	K562	blood:	n/a	n/a
2	FOXA1	chr12:56582508-56582752	T-47D	breast:	n/a	n/a
3	YY1	chr12:56582672-56583689	K562	blood:	n/a	chr12:56583411-56583420 chr12:56583235-56583255 chr12:56583457-56583471 chr12:56583423-56583437 chr12:56583405-56583419 chr12:56583412-56583423
4	SIN3A	chr12:56582408-56584283	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr12:56582658-56584985	ECC-1	luminal epithelium:	n/a	n/a
6	STAT5A	chr12:56582354-56582715	GM12878	blood:	n/a	n/a
7	MAX	chr12:56582675-56582862	GM12878	blood:	n/a	n/a
8	MAX	chr12:56582472-56584998	A549	lung:	n/a	n/a
9	WRNIP1	chr12:56581843-56582764	GM12878	blood:	n/a	n/a
10	MAX	chr12:56582540-56582867	K562	blood:	n/a	n/a
11	POLR2A	chr12:56582620-56584337	H1-hESC	embryonic stem cell:	n/a	n/a
12	HCFC1	chr12:56582463-56584828	Hela-S3	cervix:	n/a	n/a
13	RUNX3	chr12:56582318-56582731	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:56582004-56584372	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAZ	chr12:56582102-56584291	IMR90	lung:	n/a	n/a
16	UBTF	chr12:56582560-56582791	K562	blood:	n/a	n/a
17	POLR2A	chr12:56582586-56582807	Hela-S3	cervix:	n/a	n/a
18	MTA3	chr12:56581909-56582895	GM12878	blood:	n/a	n/a
19	TAF1	chr12:56582378-56582883	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr12:56582544-56582747	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:56582592-56582844	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZBTB7A	chr12:56582408-56583336	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr12:56582498-56582825	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:56582245-56582797	K562	blood:	n/a	n/a
25	TAF1	chr12:56582445-56583295	H1-hESC	embryonic stem cell:	n/a	n/a
26	ELF1	chr12:56582424-56584359	GM12878	blood:	n/a	chr12:56583454-56583463 chr12:56583411-56583420 chr12:56583461-56583473 chr12:56584070-56584079 chr12:56584068-56584081
27	STAT5A	chr12:56582241-56582825	GM12878	blood:	n/a	n/a
28	EP300	chr12:56582375-56584487	ECC-1	luminal epithelium:	n/a	chr12:56582873-56582882 chr12:56583770-56583783 chr12:56583599-56583615
29	TCF12	chr12:56582343-56584410	ECC-1	luminal epithelium:	n/a	chr12:56583067-56583077
30	ZBTB7A	chr12:56582459-56584305	ECC-1	luminal epithelium:	n/a	chr12:56583500-56583509
31	YY1	chr12:56582519-56582975	H1-hESC	embryonic stem cell:	n/a	n/a
32	FOXA2	chr12:56582564-56582775	HepG2	liver:	n/a	n/a
33	POLR2A	chr12:56582360-56583735	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr12:56582552-56582899	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr12:56582391-56583707	H1-neurons	neurons:	n/a	n/a
36	REST	chr12:56581798-56584443	H1-neurons	neurons:	n/a	chr12:56582869-56582882 chr12:56582738-56582751

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56581482..56583499-chr12:56651380..56653710,2	K562	blood:
2	chr12:56582602..56584136-chr12:56615794..56617313,2	K562	blood:
3	chr12:56438470..56440539-chr12:56581199..56583152,2	MCF-7	breast:
4	chr12:56434140..56437753-chr12:56579716..56586472,8	K562	blood:
5	chr12:56579705..56582945-chr12:57008774..57012343,3	K562	blood:
6	chr12:56511802..56513894-chr12:56582502..56584213,17	K562	blood:
7	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
8	chr12:56434274..56437218-chr12:56582509..56584521,4	MCF-7	breast:
9	chr12:56582327..56583849-chr12:56861847..56864785,2	MCF-7	breast:
10	chr12:56573305..56575645-chr12:56580157..56583977,4	MCF-7	breast:
11	chr12:56581127..56584994-chr12:56605345..56610385,5	MCF-7	breast:
12	chr12:56507991..56525761-chr12:56579808..56586137,68	MCF-7	breast:
13	chr12:56543953..56550163-chr12:56578779..56585351,11	MCF-7	breast:
14	chr12:56581557..56584767-chr12:56708519..56710789,3	K562	blood:
15	chr12:56582602..56584894-chr12:56615504..56618371,3	K562	blood:
16	chr12:56368058..56369661-chr12:56581605..56583172,2	MCF-7	breast:
17	chr12:56518236..56525779-chr12:56581707..56584752,14	MCF-7	breast:
18	chr12:56582670..56585645-chr12:56588160..56590728,3	MCF-7	breast:
19	chr12:56580530..56583816-chr12:56859558..56862740,3	K562	blood:
20	chr12:56434529..56437485-chr12:56581091..56583996,4	K562	blood:
21	chr12:56582633..56585522-chr12:56623000..56624592,2	MCF-7	breast:
22	chr12:56579883..56589030-chr12:56613342..56620091,21	MCF-7	breast:
23	chr12:56508832..56515879-chr12:56578376..56587782,37	MCF-7	breast:
24	chr12:56582213..56584132-chr12:56708371..56710862,2	MCF-7	breast:
25	chr12:56438264..56440489-chr12:56580278..56583013,2	K562	blood:
26	chr12:56576539..56578813-chr12:56582057..56584361,3	MCF-7	breast:
27	chr12:56471914..56476515-chr12:56581933..56586574,4	MCF-7	breast:
28	chr12:56579404..56590957-chr12:56614094..56620955,25	MCF-7	breast:
29	chr12:56480948..56483944-chr12:56582412..56584224,2	MCF-7	breast:
30	chr12:56471773..56473487-chr12:56580926..56582865,2	MCF-7	breast:
31	chr12:56582084..56583845-chr12:56753291..56755155,2	MCF-7	breast:
32	chr12:56582392..56584464-chr12:56753681..56756139,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMARCC2	TF binding region
ENSG00000065361	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000266023	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139540	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	esv1792521	chr12:56575188-56587576	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	esv3389557	chr12:56581710-56584658	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv3492532	chr12:56582085-56584833	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	esv3492533	chr12:56582085-56584833	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv973989	chr12:56582243-56602996	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 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	chr12:56580800-56582800	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr12:56581000-56582800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr12:56581000-56582800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:56581200-56582800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr12:56581200-56582800	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr12:56581200-56582800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:56581400-56582800	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr12:56581400-56584600	Active TSS	Fetal Kidney	kidney
9	chr12:56581400-56584800	Active TSS	Colonic Mucosa	Colon
10	chr12:56581600-56582800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr12:56581600-56582800	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr12:56581600-56582800	Flanking Active TSS	HUVEC	blood vessel
13	chr12:56581600-56582800	Flanking Active TSS	NH-A	brain
14	chr12:56581600-56583000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr12:56581800-56582800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr12:56581800-56582800	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr12:56581800-56582800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr12:56581800-56582800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:56581800-56582800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:56581800-56582800	Flanking Active TSS	Fetal Muscle Trunk	muscle
21	chr12:56581800-56582800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr12:56581800-56582800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr12:56581800-56582800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr12:56581800-56584600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr12:56582000-56582800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr12:56582000-56582800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:56582000-56582800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:56582000-56582800	Flanking Active TSS	Liver	Liver
29	chr12:56582000-56582800	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr12:56582000-56582800	Flanking Active TSS	Psoas Muscle	Psoas
31	chr12:56582000-56584600	Active TSS	GM12878-XiMat	blood
32	chr12:56582000-56584800	Active TSS	H1 Cell Line	embryonic stem cell
33	chr12:56582000-56584800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:56582000-56584800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:56582000-56584800	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr12:56582000-56584800	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr12:56582000-56584800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr12:56582000-56585000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr12:56582200-56582800	Flanking Active TSS	Placenta	Placenta
40	chr12:56582200-56583800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:56582200-56584200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:56582200-56584200	Active TSS	Aorta	Aorta
43	chr12:56582200-56584200	Active TSS	Lung	lung
44	chr12:56582200-56584200	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr12:56582200-56584400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:56582200-56584400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:56582200-56584400	Active TSS	Fetal Brain Male	brain
48	chr12:56582200-56584400	Active TSS	Fetal Brain Female	brain
49	chr12:56582200-56584400	Active TSS	A549	lung
50	chr12:56582200-56584400	Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links