Variant report

Variant	rs2448945
Chromosome Location	chr15:52107123-52107124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52105030..52107341-chr15:52262781..52264487,2	MCF-7	breast:
2	chr15:52100222..52103696-chr15:52103888..52107125,3	MCF-7	breast:
3	chr15:52093017..52094585-chr15:52106395..52107997,2	MCF-7	breast:
4	chr15:52105390..52107839-chr15:52134954..52136621,2	K562	blood:
5	chr15:52097000..52098593-chr15:52105503..52107331,2	K562	blood:
6	chr15:52100848..52103641-chr15:52104210..52107534,4	K562	blood:
7	chr15:52106284..52108941-chr15:52129387..52131261,2	MCF-7	breast:
8	chr15:52103958..52107915-chr15:52115684..52119713,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1133878	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16964482	1.00[CHB][hapmap]
rs16964483	1.00[CHB][hapmap]
rs17611465	1.00[CHB][hapmap]
rs1863429	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1972419	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1991267	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs2016057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2124587	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2258248	1.00[CHB][hapmap]
rs2448810	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2554354	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2554355	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2554358	0.96[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2570230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2570243	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2593169	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2593181	1.00[CHB][hapmap]
rs2593184	0.83[AMR][1000 genomes]
rs2606128	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2606130	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2606133	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2606147	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2622765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2622778	1.00[CHB][hapmap]
rs2623245	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2623247	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2623251	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2623258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2623263	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2623270	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2652595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2652597	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2959296	1.00[CHB][hapmap]
rs691738	0.86[AMR][1000 genomes];0.99[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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv3361968	chr15:52087428-52107237	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2448945	SCG3	cis	Brain Pons	GTEx
rs2448945	SCG3	cis	Temporal Cortex	GTEx
rs2448945	SCG3	cis	Cerebellum	GTEx
rs2448945	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52061600-52112000	Weak transcription	NHLF	lung
2	chr15:52085800-52108800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:52089200-52107200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:52091200-52109400	Weak transcription	Gastric	stomach
5	chr15:52091800-52108200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:52092000-52107800	Weak transcription	Fetal Muscle Leg	muscle
7	chr15:52093800-52108600	Weak transcription	Fetal Lung	lung
8	chr15:52098800-52108800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr15:52099200-52107400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:52099200-52108800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:52099400-52107200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr15:52099600-52108600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr15:52099600-52108800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr15:52099800-52108400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:52099800-52109000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:52099800-52109400	Weak transcription	Spleen	Spleen
17	chr15:52099800-52110000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:52099800-52110400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:52099800-52110400	Weak transcription	Left Ventricle	heart
20	chr15:52099800-52113800	Weak transcription	Aorta	Aorta
21	chr15:52100000-52109400	Weak transcription	Esophagus	oesophagus
22	chr15:52100000-52109400	Weak transcription	Fetal Stomach	stomach
23	chr15:52100000-52109400	Weak transcription	Lung	lung
24	chr15:52100000-52110200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:52100000-52113200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:52100200-52109400	Weak transcription	Fetal Brain Female	brain
27	chr15:52100400-52108400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:52100600-52109800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:52101000-52107200	Weak transcription	Fetal Thymus	thymus
30	chr15:52101200-52108800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:52101200-52110200	Weak transcription	NHDF-Ad	bronchial
32	chr15:52101600-52113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:52101800-52110200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:52102000-52108400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:52102000-52108400	Weak transcription	Brain Substantia Nigra	brain
36	chr15:52102000-52113400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:52102400-52108200	Weak transcription	Fetal Intestine Large	intestine
38	chr15:52102400-52109000	Weak transcription	Adipose Nuclei	Adipose
39	chr15:52103000-52108000	Weak transcription	Fetal Intestine Small	intestine
40	chr15:52103000-52109000	Weak transcription	Colon Smooth Muscle	Colon
41	chr15:52103000-52111600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr15:52104000-52107600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:52104400-52113400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:52104400-52113600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:52105600-52113200	Weak transcription	Primary B cells from cord blood	blood
46	chr15:52105800-52107200	Strong transcription	Brain Angular Gyrus	brain
47	chr15:52105800-52107200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:52105800-52107600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:52105800-52111600	Weak transcription	Thymus	Thymus
50	chr15:52106600-52111800	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links