Variant report

Variant	rs12323939
Chromosome Location	chr15:41137177-41137178
allele	C/G
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	TCF12	chr15:41136163-41137360	ECC-1	luminal epithelium:	n/a	n/a
2	SIN3AK20	chr15:41135955-41137422	MCF-7	breast:	n/a	n/a
3	YY1	chr15:41136707-41137382	H1-hESC	embryonic stem cell:	n/a	chr15:41136760-41136780
4	MAX	chr15:41136186-41137423	ECC-1	luminal epithelium:	n/a	chr15:41136188-41136198
5	ELF1	chr15:41135827-41137451	GM12878	blood:	n/a	chr15:41136197-41136206 chr15:41136192-41136204 chr15:41135983-41135995
6	RUNX3	chr15:41136400-41137296	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:41135422-41137445	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr15:41136865-41137214	GM12878	blood:	n/a	n/a
9	EP300	chr15:41136081-41137354	ECC-1	luminal epithelium:	n/a	chr15:41136085-41136101 chr15:41136086-41136102 chr15:41136417-41136433 chr15:41136179-41136195
10	CTCF	chr15:41137080-41137230	HMEC	breast:	n/a	n/a
11	POLR2A	chr15:41135645-41137310	MCF-7	breast:	n/a	n/a
12	YY1	chr15:41136844-41137342	ECC-1	luminal epithelium:	n/a	n/a
13	YY1	chr15:41136510-41137274	GM12892	blood:	n/a	chr15:41136760-41136780
14	TAF1	chr15:41135862-41137255	ECC-1	luminal epithelium:	n/a	n/a
15	YY1	chr15:41136207-41137274	ECC-1	luminal epithelium:	n/a	chr15:41136760-41136780
16	POLR2A	chr15:41136764-41137247	GM12892	blood:	n/a	n/a
17	TAF1	chr15:41135745-41137209	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr15:41135442-41137369	HCT-116	colon:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
19	YY1	chr15:41136685-41137252	GM12878	blood:	n/a	chr15:41136760-41136780
20	POLR2A	chr15:41135995-41137213	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF12	chr15:41136011-41137345	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr15:41136761-41137214	GM12878	blood:	n/a	n/a
23	ZNF263	chr15:41136269-41137186	K562	blood:	n/a	chr15:41136590-41136611 chr15:41136740-41136749 chr15:41136590-41136599
24	TEAD4	chr15:41136160-41137347	ECC-1	luminal epithelium:	n/a	n/a
25	PML	chr15:41136766-41137253	GM12878	blood:	n/a	n/a
26	CEBPB	chr15:41137176-41137511	MCF-7	breast:	n/a	chr15:41137401-41137412
27	MXI1	chr15:41136834-41137208	H1-hESC	embryonic stem cell:	n/a	n/a
28	ZBTB7A	chr15:41136188-41137205	ECC-1	luminal epithelium:	n/a	chr15:41136391-41136399
29	POLR2A	chr15:41136833-41137204	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr15:41136917-41137241	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr15:41136907-41137236	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr15:41136902-41137226	GM12891	blood:	n/a	n/a
33	ZBTB7A	chr15:41135746-41137301	ECC-1	luminal epithelium:	n/a	chr15:41136391-41136399
34	POLR2A	chr15:41135481-41137236	ECC-1	luminal epithelium:	n/a	n/a
35	MTA3	chr15:41136254-41137415	GM12878	blood:	n/a	n/a
36	RUNX3	chr15:41136776-41137221	GM12878	blood:	n/a	n/a
37	MAX	chr15:41136146-41137247	H1-hESC	embryonic stem cell:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
38	ZEB1	chr15:41135490-41137303	GM12878	blood:	n/a	chr15:41135832-41135843 chr15:41136372-41136379 chr15:41136370-41136379 chr15:41136646-41136657
39	MAX	chr15:41136903-41137305	NB4	blood:	n/a	n/a
40	MAX	chr15:41136130-41137323	MCF-7	breast:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
41	POLR2A	chr15:41137065-41137262	ProgFib	skin:	n/a	n/a
42	HA-E2F1	chr15:41136258-41137343	MCF-7	breast:	n/a	chr15:41136420-41136429
43	TBP	chr15:41136006-41137186	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr15:41135935-41137248	MCF-7	breast:	n/a	n/a
45	PAX5	chr15:41136696-41137183	GM12892	blood:	n/a	n/a
46	SIN3A	chr15:41135543-41137347	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAX	chr15:41136097-41137317	H1-hESC	embryonic stem cell:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
48	CTCF	chr15:41137100-41137250	HCPEpiC	choroid plexus:	n/a	n/a
49	MAX	chr15:41136145-41137357	ECC-1	luminal epithelium:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
50	CHD1	chr15:41137015-41137443	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
2	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
3	chr15:41036541..41039505-chr15:41136514..41138272,3	MCF-7	breast:
4	chr15:41135781..41139367-chr15:41195514..41200270,4	MCF-7	breast:
5	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
6	chr15:41045671..41048162-chr15:41135920..41137784,2	MCF-7	breast:
7	chr15:41120065..41123435-chr15:41135561..41137302,3	MCF-7	breast:
8	chr15:41099271..41102222-chr15:41135281..41137187,2	K562	blood:
9	chr15:41098123..41102222-chr15:41134582..41138137,4	K562	blood:
10	chr15:41135103..41140677-chr15:41182913..41189081,12	MCF-7	breast:
11	chr15:41129275..41132805-chr15:41134409..41137816,5	MCF-7	breast:
12	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261183	TF binding region
ENSG00000166140	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000166143	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000104129	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10220885	1.00[EUR][1000 genomes]
rs16971119	1.00[EUR][1000 genomes]
rs45494798	1.00[AMR][1000 genomes]
rs45501094	1.00[EUR][1000 genomes]
rs45571032	1.00[EUR][1000 genomes]
rs45604436	1.00[EUR][1000 genomes]
rs55896567	1.00[EUR][1000 genomes]
rs55906732	1.00[EUR][1000 genomes]
rs56229816	1.00[EUR][1000 genomes]
rs57242620	1.00[EUR][1000 genomes]
rs57288992	1.00[EUR][1000 genomes]
rs58097169	1.00[EUR][1000 genomes]
rs58375351	1.00[EUR][1000 genomes]
rs58681580	1.00[EUR][1000 genomes]
rs58738238	1.00[EUR][1000 genomes]
rs59154296	1.00[AMR][1000 genomes]
rs59508492	1.00[EUR][1000 genomes]
rs59528823	1.00[EUR][1000 genomes]
rs59558714	1.00[EUR][1000 genomes]
rs60109064	1.00[EUR][1000 genomes]
rs60111609	1.00[EUR][1000 genomes]
rs60163307	1.00[EUR][1000 genomes]
rs60223077	1.00[AMR][1000 genomes]
rs60578270	1.00[EUR][1000 genomes]
rs60822673	1.00[EUR][1000 genomes]
rs6492962	1.00[EUR][1000 genomes]
rs6492963	1.00[EUR][1000 genomes]
rs7161941	1.00[EUR][1000 genomes]
rs7164574	1.00[EUR][1000 genomes]
rs7166733	1.00[EUR][1000 genomes]
rs7167831	1.00[EUR][1000 genomes]
rs7168217	1.00[EUR][1000 genomes]
rs7169273	1.00[EUR][1000 genomes]
rs7171451	1.00[EUR][1000 genomes]
rs7171898	1.00[EUR][1000 genomes]
rs7172356	1.00[EUR][1000 genomes]
rs7178058	1.00[EUR][1000 genomes]
rs7178244	1.00[EUR][1000 genomes]
rs7182066	1.00[EUR][1000 genomes]
rs7182516	1.00[EUR][1000 genomes]
rs73394786	1.00[AMR][1000 genomes]
rs73396569	1.00[AMR][1000 genomes]
rs73396577	1.00[AMR][1000 genomes]
rs74011880	1.00[EUR][1000 genomes]
rs74011881	1.00[EUR][1000 genomes]
rs74011884	1.00[EUR][1000 genomes]
rs74011886	1.00[EUR][1000 genomes]
rs74011887	1.00[EUR][1000 genomes]
rs74011888	1.00[EUR][1000 genomes]
rs74011933	1.00[EUR][1000 genomes]
rs74011936	1.00[EUR][1000 genomes]
rs8035580	1.00[EUR][1000 genomes]
rs8038751	1.00[EUR][1000 genomes]
rs8039169	1.00[EUR][1000 genomes]
rs8039942	1.00[EUR][1000 genomes]
rs8040579	1.00[EUR][1000 genomes]
rs8040925	1.00[EUR][1000 genomes]
rs9672224	1.00[EUR][1000 genomes]
rs9744142	1.00[EUR][1000 genomes]

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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41135200-41137800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr15:41135200-41138800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:41135200-41139000	Active TSS	Fetal Kidney	kidney
4	chr15:41135400-41137400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:41135400-41137600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:41135600-41137200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
7	chr15:41135600-41137200	Flanking Active TSS	Colonic Mucosa	Colon
8	chr15:41135600-41137200	Active TSS	Small Intestine	intestine
9	chr15:41135600-41137400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:41135600-41137400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:41135600-41137400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr15:41135600-41137600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr15:41135600-41137600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:41135600-41137600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr15:41135600-41137600	Active TSS	Placenta Amnion	Placenta Amnion
16	chr15:41135600-41138200	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr15:41135600-41138400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr15:41135600-41138400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:41135600-41138600	Active TSS	Gastric	stomach
20	chr15:41135600-41140200	Active TSS	Rectal Smooth Muscle	rectum
21	chr15:41135600-41140400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:41135800-41137200	Active TSS	Ovary	ovary
23	chr15:41135800-41137400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr15:41135800-41137400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr15:41135800-41137400	Bivalent Enhancer	Fetal Brain Male	brain
26	chr15:41135800-41137400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
27	chr15:41135800-41137400	Flanking Active TSS	Right Ventricle	heart
28	chr15:41135800-41137400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
29	chr15:41135800-41137600	Active TSS	H1 Cell Line	embryonic stem cell
30	chr15:41135800-41137600	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr15:41135800-41137600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
32	chr15:41135800-41137600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr15:41135800-41137600	Active TSS	NHEK	skin
34	chr15:41135800-41137800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:41135800-41137800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr15:41135800-41137800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:41135800-41137800	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr15:41135800-41138200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr15:41135800-41138800	Active TSS	Esophagus	oesophagus
40	chr15:41136000-41137200	Active TSS	Primary T cells from cord blood	blood
41	chr15:41136000-41137200	Flanking Bivalent TSS/Enh	Thymus	Thymus
42	chr15:41136000-41137400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:41136000-41137600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:41136000-41137600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:41136000-41137600	Active TSS	Pancreas	Pancrea
46	chr15:41136000-41137800	Active TSS	HMEC	breast
47	chr15:41136000-41138400	Active TSS	Stomach Mucosa	stomach
48	chr15:41136200-41137200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:41136200-41137200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:41136200-41137200	Active TSS	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links