Variant report

Variant	rs58954461
Chromosome Location	chr15:75303449-75303450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75300826..75305111-chr15:75313603..75318752,6	MCF-7	breast:
2	chr15:75287065..75288881-chr15:75303278..75305678,2	MCF-7	breast:
3	chr15:75302980..75304655-chr15:75315027..75317604,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPP25-2	chr15:75303307-75304737	ucscGeneNc_uc002bcp_2

Variant related genes	Relation type
ENSG00000198794	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000260483	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16973530	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59423613	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7173752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73432970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73438515	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73438534	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73438559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75289400-75305000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:75289400-75305000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:75289400-75305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
6	chr15:75289600-75304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:75289600-75305400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:75289800-75304000	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:75290000-75303600	Weak transcription	Brain Angular Gyrus	brain
10	chr15:75290000-75303800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:75290000-75304400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:75290000-75304400	Weak transcription	HepG2	liver
13	chr15:75290000-75309400	Weak transcription	Gastric	stomach
14	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
15	chr15:75290400-75304800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:75290400-75304800	Weak transcription	Brain Anterior Caudate	brain
17	chr15:75290600-75304400	Weak transcription	Fetal Stomach	stomach
18	chr15:75291400-75305400	Weak transcription	Fetal Brain Male	brain
19	chr15:75292000-75305000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:75292600-75305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:75293000-75304000	Weak transcription	Fetal Intestine Large	intestine
22	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:75294600-75312200	Weak transcription	Adipose Nuclei	Adipose
24	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:75296800-75303600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:75297200-75304600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:75297400-75305000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:75297600-75303800	Weak transcription	Fetal Brain Female	brain
29	chr15:75298200-75304000	Weak transcription	Pancreas	Pancrea
30	chr15:75298200-75305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:75300200-75304000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:75300200-75304200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:75300400-75304400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:75300400-75304600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:75300400-75312200	Weak transcription	Spleen	Spleen
36	chr15:75301000-75315400	Weak transcription	Thymus	Thymus
37	chr15:75301800-75304800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:75301800-75306600	Weak transcription	Placenta	Placenta
39	chr15:75302000-75314000	Strong transcription	Fetal Intestine Small	intestine
40	chr15:75302200-75313200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:75302200-75313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:75302400-75304000	Bivalent Enhancer	Primary B cells from cord blood	blood
43	chr15:75302600-75304200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr15:75302800-75303800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:75303000-75303600	Weak transcription	Brain Germinal Matrix	brain
46	chr15:75303000-75304000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:75303200-75303600	Weak transcription	GM12878-XiMat	blood
48	chr15:75303400-75305200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links