Variant report

Variant	rs56400389
Chromosome Location	chr15:41230536-41230537
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41198454..41200514-chr15:41229718..41231827,2	MCF-7	breast:
2	chr15:41210690..41212300-chr15:41230251..41232745,2	MCF-7	breast:
3	chr15:41196271..41197123-chr15:41230429..41231022,2	MCF-7	breast:
4	chr15:41227314..41231874-chr15:41244073..41246571,4	MCF-7	breast:
5	chr15:41230478..41233329-chr15:41297882..41299703,2	MCF-7	breast:
6	chr15:41229339..41231182-chr15:41247878..41250460,2	MCF-7	breast:
7	chr15:41230302..41232143-chr15:41307397..41311202,3	MCF-7	breast:
8	chr15:41229926..41230909-chr15:41310448..41311427,5	MCF-7	breast:
9	chr15:41229330..41231343-chr15:41257972..41259697,2	MCF-7	breast:
10	chr15:41229929..41230873-chr15:41310737..41311759,3	MCF-7	breast:
11	chr15:41230059..41232086-chr15:41262058..41264861,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128965	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000259521	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10467973	1.00[AFR][1000 genomes]
rs28568593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55805015	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56038127	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57390752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73399657	0.83[AMR][1000 genomes]
rs73402523	0.85[AMR][1000 genomes]
rs73402524	0.85[AMR][1000 genomes]
rs74014718	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	esv1819792	chr15:41184722-41234825	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv904106	chr15:41221067-41259523	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41224400-41231400	Weak transcription	HUVEC	blood vessel
2	chr15:41224800-41230800	Enhancers	Liver	Liver
3	chr15:41225000-41233600	Weak transcription	Esophagus	oesophagus
4	chr15:41225600-41232400	Weak transcription	Brain Anterior Caudate	brain
5	chr15:41225800-41231400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:41225800-41231400	Strong transcription	Fetal Stomach	stomach
7	chr15:41226000-41232000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr15:41226000-41232200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:41226000-41232600	Weak transcription	Brain Angular Gyrus	brain
10	chr15:41226000-41233000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:41226000-41233400	Weak transcription	Thymus	Thymus
12	chr15:41226600-41231000	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr15:41227200-41231600	Strong transcription	Fetal Intestine Large	intestine
14	chr15:41227400-41231000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:41227800-41232400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:41227800-41233600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:41228000-41233200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:41228400-41230600	Genic enhancers	Spleen	Spleen
19	chr15:41228400-41231000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:41228400-41231000	Enhancers	Left Ventricle	heart
21	chr15:41228400-41232400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:41228600-41230600	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
23	chr15:41228600-41230800	Enhancers	Psoas Muscle	Psoas
24	chr15:41228600-41233600	Enhancers	Fetal Thymus	thymus
25	chr15:41228800-41232200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:41229200-41232400	Weak transcription	Colonic Mucosa	Colon
27	chr15:41229200-41232600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:41229400-41230800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:41229400-41232000	Strong transcription	Fetal Intestine Small	intestine
30	chr15:41229600-41230600	Enhancers	Fetal Heart	heart
31	chr15:41229600-41230600	Genic enhancers	Rectal Mucosa Donor 29	rectum
32	chr15:41229600-41231000	Genic enhancers	Lung	lung
33	chr15:41229600-41233400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:41229800-41230600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:41229800-41231000	Enhancers	Right Atrium	heart
36	chr15:41229800-41231200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:41229800-41232000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:41229800-41232400	Weak transcription	NHLF	lung
39	chr15:41230000-41230600	Enhancers	Stomach Smooth Muscle	stomach
40	chr15:41230000-41230800	Enhancers	A549	lung
41	chr15:41230000-41231000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:41230000-41231000	Enhancers	Fetal Muscle Leg	muscle
43	chr15:41230000-41232400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:41230000-41232600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:41230000-41232600	Weak transcription	HSMM	muscle
46	chr15:41230000-41232800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:41230000-41233000	Weak transcription	HSMMtube	muscle
48	chr15:41230000-41233400	Weak transcription	Osteobl	bone
49	chr15:41230200-41230800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:41230200-41230800	Strong transcription	Gastric	stomach

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