Variant report

Variant	rs12462536
Chromosome Location	chr19:45690775-45690776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr19:45690724-45691231	A549	lung:	n/a	n/a
2	RAD21	chr19:45690673-45691203	ECC-1	luminal epithelium:	n/a	n/a
3	RAD21	chr19:45690649-45691258	HCT-116	colon:	n/a	n/a
4	CTCF	chr19:45690734-45691175	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr19:45690688-45691158	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr19:45690534-45691268	HCT-116	colon:	n/a	n/a
7	CTCF	chr19:45690730-45691166	A549	lung:	n/a	n/a
8	TEAD4	chr19:45690674-45691147	ECC-1	luminal epithelium:	n/a	n/a
9	RAD21	chr19:45690669-45691121	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr19:45690748-45691169	MCF-7	breast:	n/a	n/a
11	CTCF	chr19:45690681-45691156	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr19:45690685-45691089	HepG2	liver:	n/a	n/a
13	CTCF	chr19:45690767-45691103	GM19238	blood:	n/a	n/a
14	TCF12	chr19:45690564-45691183	A549	lung:	n/a	n/a
15	TEAD4	chr19:45690742-45691204	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr19:45690752-45691147	K562	blood:	n/a	n/a
17	RAD21	chr19:45690764-45691137	H1-hESC	embryonic stem cell:	n/a	n/a
18	GTF2F1	chr19:45690769-45691049	H1-hESC	embryonic stem cell:	n/a	n/a
19	SMC3	chr19:45690726-45691170	GM12878	blood:	n/a	n/a
20	YY1	chr19:45690770-45691133	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr19:45690632-45691143	K562	blood:	n/a	n/a
22	RAD21	chr19:45690662-45691186	MCF-7	breast:	n/a	n/a
23	CTCF	chr19:45690774-45691170	K562	blood:	n/a	n/a
24	CTCF	chr19:45690555-45691166	HCT-116	colon:	n/a	n/a
25	RAD21	chr19:45690756-45691052	MCF-7	breast:	n/a	n/a
26	RAD21	chr19:45690729-45691166	HepG2	liver:	n/a	n/a
27	RAD21	chr19:45690568-45691350	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr19:45690749-45691165	GM12878	blood:	n/a	n/a
29	WRNIP1	chr19:45690746-45690957	GM12878	blood:	n/a	n/a
30	ZBTB7A	chr19:45690765-45691212	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr19:45690558-45691353	SK-N-SH	brain:	n/a	n/a
32	MTA3	chr19:45690498-45691038	GM12878	blood:	n/a	n/a
33	ESRRA	chr19:45690613-45691210	GM12878	blood:	n/a	n/a
34	RAD21	chr19:45690746-45691136	GM12878	blood:	n/a	n/a
35	RAD21	chr19:45690764-45691027	GM12878	blood:	n/a	n/a
36	RAD21	chr19:45690773-45691133	Hela-S3	cervix:	n/a	n/a
37	SMC3	chr19:45690772-45691142	Hela-S3	cervix:	n/a	n/a
38	SMC3	chr19:45690599-45691394	SK-N-SH	brain:	n/a	n/a
39	RAD21	chr19:45690738-45691129	HepG2	liver:	n/a	n/a
40	RAD21	chr19:45690705-45691095	HepG2	liver:	n/a	n/a
41	CTCF	chr19:45690762-45691108	K562	blood:	n/a	n/a
42	TEAD4	chr19:45690763-45691121	H1-hESC	embryonic stem cell:	n/a	n/a
43	RAD21	chr19:45690755-45691155	SK-N-SH_RA	brain:	n/a	n/a
44	RAD21	chr19:45690654-45691172	A549	lung:	n/a	n/a
45	CTCF	chr19:45690217-45691473	A549	lung:	n/a	n/a
46	RAD21	chr19:45690755-45691148	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45663246..45665913-chr19:45689234..45691618,2	MCF-7	breast:
2	chr19:45681420..45684587-chr19:45687242..45692393,7	MCF-7	breast:
3	chr19:45680559..45684359-chr19:45688843..45692525,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225157	TF binding region
ENSG00000189114	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000179846	Chromatin interaction
ENSG00000267545	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10415850	0.95[ASN][1000 genomes]
rs10417602	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs1048699	1.00[CEU][hapmap]
rs1114831	1.00[CEU][hapmap]
rs17643262	1.00[CEU][hapmap]
rs59839536	0.92[ASN][1000 genomes]
rs7247764	0.88[JPT][hapmap]

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	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription 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 target site	36 gene(s)	inside rSNPs	diseases
2	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1794498	chr19:45673701-45691040	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv2422482	chr19:45676705-45769805	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1794901	chr19:45681661-45690775	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv833844	chr19:45684309-45887406	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45683400-45690800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:45683400-45693200	Weak transcription	Aorta	Aorta
3	chr19:45684000-45695200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:45684800-45690800	Weak transcription	Colonic Mucosa	Colon
5	chr19:45684800-45690800	Weak transcription	Fetal Brain Female	brain
6	chr19:45684800-45691200	Weak transcription	Right Atrium	heart
7	chr19:45684800-45696000	Weak transcription	Fetal Intestine Large	intestine
8	chr19:45684800-45697600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:45684800-45701000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:45684800-45715000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:45685000-45690800	Weak transcription	Adipose Nuclei	Adipose
12	chr19:45685000-45690800	Weak transcription	Gastric	stomach
13	chr19:45685000-45695000	Weak transcription	Ovary	ovary
14	chr19:45685000-45698600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:45685000-45699000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:45685000-45704600	Weak transcription	Esophagus	oesophagus
17	chr19:45685000-45705600	Weak transcription	Lung	lung
18	chr19:45685000-45705800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:45685200-45690800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:45685200-45690800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr19:45685200-45690800	Weak transcription	Placenta	Placenta
22	chr19:45685200-45698800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr19:45685400-45690800	Weak transcription	Fetal Muscle Leg	muscle
24	chr19:45685600-45694800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:45685600-45696200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:45685800-45690800	Weak transcription	Fetal Stomach	stomach
27	chr19:45686400-45694800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:45686400-45694800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:45686400-45694800	Weak transcription	NHEK	skin
30	chr19:45686600-45699000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr19:45687000-45692800	Weak transcription	Fetal Intestine Small	intestine
32	chr19:45687600-45695400	Weak transcription	K562	blood
33	chr19:45690000-45691000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:45690000-45691000	Enhancers	Spleen	Spleen
35	chr19:45690200-45690800	Enhancers	Liver	Liver
36	chr19:45690200-45690800	Weak transcription	Osteobl	bone
37	chr19:45690400-45690800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:45690400-45690800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:45690400-45691000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:45690400-45691000	Enhancers	Pancreas	Pancrea
41	chr19:45690600-45690800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr19:45690600-45690800	Enhancers	Primary B cells from cord blood	blood
43	chr19:45690600-45690800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr19:45690600-45690800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:45690600-45690800	Enhancers	Left Ventricle	heart
46	chr19:45690600-45690800	Enhancers	Stomach Mucosa	stomach
47	chr19:45690600-45691000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:45690600-45691000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr19:45690600-45691000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
50	chr19:45690600-45691000	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links