Variant report

Variant	rs12900515
Chromosome Location	chr15:55698788-55698789
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr15:55698741-55698892	K562	blood:	n/a	n/a
2	TBP	chr15:55698785-55699184	K562	blood:	n/a	n/a
3	GATA1	chr15:55698013-55698890	PBDE	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55696852..55699665-chr15:55712534..55714960,2	K562	blood:
2	chr15:55609877..55611698-chr15:55698360..55701817,3	MCF-7	breast:
3	chr13:29973836..29976815-chr15:55698261..55699841,2	K562	blood:
4	chr15:55487401..55489256-chr15:55698750..55700399,2	MCF-7	breast:
5	chr15:55486571..55489386-chr15:55698193..55701285,4	K562	blood:
6	chr15:55486571..55488270-chr15:55698193..55700233,2	K562	blood:
7	chr15:55698446..55701018-chr15:55709702..55712524,2	MCF-7	breast:
8	chr15:55608625..55613147-chr15:55698683..55702764,8	MCF-7	breast:
9	chr15:55607682..55613892-chr15:55697623..55703247,7	K562	blood:
10	chr15:55694340..55696767-chr15:55697475..55699670,2	MCF-7	breast:

No data

Variant related genes	Relation type
C15orf65	TF binding region
ENSG00000069974	Chromatin interaction
ENSG00000137876	Chromatin interaction
ENSG00000225973	Chromatin interaction
ENSG00000069943	Chromatin interaction
ENSG00000261652	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11855303	1.00[AMR][1000 genomes]
rs12914468	1.00[AMR][1000 genomes]
rs4553564	1.00[AMR][1000 genomes]
rs6493782	1.00[AMR][1000 genomes]
rs6493784	1.00[AMR][1000 genomes]
rs7162868	1.00[AMR][1000 genomes]
rs7169473	1.00[AMR][1000 genomes]
rs7169776	1.00[AMR][1000 genomes]
rs73411059	1.00[AMR][1000 genomes]
rs8029091	1.00[AMR][1000 genomes]
rs8029172	1.00[AMR][1000 genomes]
rs8039104	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription 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 miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv520799	chr15:55645661-55760522	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv904244	chr15:55687969-55770911	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
2	chr15:55637000-55699600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:55668200-55699800	Weak transcription	Spleen	Spleen
4	chr15:55676000-55699400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:55676400-55699400	Weak transcription	Right Ventricle	heart
6	chr15:55678200-55699400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:55681000-55699200	Weak transcription	Lung	lung
8	chr15:55681000-55699600	Weak transcription	Fetal Stomach	stomach
9	chr15:55681200-55699400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:55681800-55699600	Weak transcription	NHLF	lung
11	chr15:55687400-55699400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:55687400-55699400	Weak transcription	Fetal Brain Female	brain
13	chr15:55687400-55699600	Weak transcription	Left Ventricle	heart
14	chr15:55689800-55699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:55691800-55699400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr15:55694600-55698800	Enhancers	Hela-S3	cervix
17	chr15:55694800-55698800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:55695000-55699400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr15:55695000-55699600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr15:55695000-55699600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr15:55695200-55699200	Weak transcription	Small Intestine	intestine
22	chr15:55695600-55699400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr15:55696000-55699000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:55696000-55699000	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:55696000-55699400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:55696200-55699000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:55696200-55699400	Weak transcription	Fetal Lung	lung
28	chr15:55696200-55699400	Weak transcription	NHEK	skin
29	chr15:55696200-55699600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:55696200-55699600	Weak transcription	Fetal Intestine Small	intestine
31	chr15:55696400-55698800	Enhancers	Dnd41	blood
32	chr15:55696400-55699400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:55696400-55699400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:55696400-55699400	Weak transcription	Brain Angular Gyrus	brain
35	chr15:55696400-55699400	Weak transcription	Brain Anterior Caudate	brain
36	chr15:55696400-55699400	Weak transcription	Osteobl	bone
37	chr15:55696400-55699600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:55696600-55698800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:55696600-55699400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:55696600-55699400	Enhancers	Primary hematopoietic stem cells	blood
41	chr15:55696600-55699400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:55696600-55699400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr15:55696600-55699600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:55696600-55699800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr15:55696800-55699000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr15:55696800-55699400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr15:55696800-55699400	Enhancers	GM12878-XiMat	blood
48	chr15:55696800-55699400	Weak transcription	HUVEC	blood vessel
49	chr15:55696800-55699600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:55696800-55699600	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links