Variant report

Variant	rs960026
Chromosome Location	chr15:59702856-59702857
allele	A/C
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	CEBPB	chr15:59702606-59702861	A549	lung:	n/a	n/a
2	TCF12	chr15:59702343-59703369	A549	lung:	n/a	n/a
3	NR3C1	chr15:59702535-59702999	A549	lung:	n/a	n/a
4	SP1	chr15:59702466-59703257	A549	lung:	n/a	n/a
5	SMC3	chr15:59702702-59702965	GM12878	blood:	n/a	n/a
6	FOXA2	chr15:59702510-59703239	A549	lung:	n/a	n/a
7	RUNX3	chr15:59702508-59703114	GM12878	blood:	n/a	n/a
8	IKZF1	chr15:59702353-59703017	GM12878	blood:	n/a	n/a
9	EP300	chr15:59702637-59702977	GM12878	blood:	n/a	n/a
10	MTA3	chr15:59702461-59703184	GM12878	blood:	n/a	n/a
11	EBF1	chr15:59702653-59703005	GM12878	blood:	n/a	n/a
12	FOSL2	chr15:59702475-59703222	A549	lung:	n/a	n/a
13	TBP	chr15:59702523-59703061	GM12878	blood:	n/a	n/a
14	SP1	chr15:59702401-59703135	A549	lung:	n/a	n/a
15	RELA	chr15:59702513-59703183	GM19099	blood:	n/a	n/a
16	RELA	chr15:59702600-59703060	GM19193	blood:	n/a	n/a
17	RUNX3	chr15:59702607-59702993	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000259674	TF binding region

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1385115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16941480	1.00[EUR][1000 genomes]
rs61340984	1.00[EUR][1000 genomes]
rs73432622	1.00[EUR][1000 genomes]
rs73432625	1.00[EUR][1000 genomes]
rs8024829	1.00[EUR][1000 genomes]
rs8037050	1.00[EUR][1000 genomes]
rs923012	1.00[EUR][1000 genomes]
rs960025	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv904275	chr15:59648633-59726610	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
4	nsv904276	chr15:59648633-59743010	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a
5	nsv904277	chr15:59666992-59705005	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
6	nsv524569	chr15:59666992-59712427	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59675200-59703000	Weak transcription	Aorta	Aorta
2	chr15:59692800-59704800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:59693000-59704800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:59693000-59704800	Weak transcription	Spleen	Spleen
5	chr15:59693000-59705000	Weak transcription	Fetal Thymus	thymus
6	chr15:59695200-59707000	Enhancers	Primary B cells from peripheral blood	blood
7	chr15:59699200-59706400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr15:59699400-59704200	Enhancers	Primary B cells from cord blood	blood
9	chr15:59699400-59705200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:59700200-59704200	Weak transcription	Placenta	Placenta
11	chr15:59700400-59705200	Weak transcription	Pancreas	Pancrea
12	chr15:59701400-59703600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:59701400-59706000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr15:59702200-59703000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr15:59702200-59703000	Enhancers	Colonic Mucosa	Colon
16	chr15:59702200-59703000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr15:59702200-59703200	Enhancers	Fetal Intestine Small	intestine
18	chr15:59702200-59703400	Enhancers	Fetal Intestine Large	intestine
19	chr15:59702200-59703600	Enhancers	Primary hematopoietic stem cells	blood
20	chr15:59702200-59703600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:59702200-59706000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:59702400-59703000	Enhancers	Duodenum Mucosa	Duodenum
23	chr15:59702400-59703200	Enhancers	Stomach Mucosa	stomach
24	chr15:59702400-59703600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr15:59702400-59703600	Flanking Active TSS	A549	lung
26	chr15:59702400-59703600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr15:59702400-59704000	Enhancers	Fetal Kidney	kidney
28	chr15:59702600-59703000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr15:59702600-59703000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:59702600-59703000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:59702600-59703000	Flanking Active TSS	Liver	Liver
32	chr15:59702600-59703000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr15:59702600-59703000	Flanking Active TSS	GM12878-XiMat	blood
34	chr15:59702600-59703000	Flanking Active TSS	HepG2	liver
35	chr15:59702600-59703800	Enhancers	Adipose Nuclei	Adipose
36	chr15:59702800-59703000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr15:59702800-59703200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr15:59702800-59703400	Weak transcription	Left Ventricle	heart
39	chr15:59702800-59704200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:59702800-59704800	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links