Variant report

Variant	rs56879579
Chromosome Location	chr15:51737777-51737778
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51737006..51738600-chr15:51770041..51772007,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10519310	0.89[ASN][1000 genomes]
rs10851501	0.85[EUR][1000 genomes]
rs11070861	0.87[EUR][1000 genomes]
rs11857716	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12324531	0.85[EUR][1000 genomes]
rs12441057	0.87[EUR][1000 genomes]
rs12708427	0.86[EUR][1000 genomes]
rs12904173	0.88[EUR][1000 genomes]
rs12904583	0.90[EUR][1000 genomes]
rs1378894	0.85[EUR][1000 genomes]
rs1378895	0.85[EUR][1000 genomes]
rs1551657	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1599034	1.00[ASN][1000 genomes]
rs16964389	0.89[ASN][1000 genomes]
rs17524750	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17524906	0.88[EUR][1000 genomes]
rs1902595	0.86[EUR][1000 genomes]
rs1902596	0.86[EUR][1000 genomes]
rs2061425	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2252220	0.85[EUR][1000 genomes]
rs2271674	1.00[ASN][1000 genomes]
rs2414112	0.86[EUR][1000 genomes]
rs2606141	0.81[EUR][1000 genomes]
rs2606143	0.85[EUR][1000 genomes]
rs28408214	0.85[EUR][1000 genomes]
rs34448759	0.90[EUR][1000 genomes]
rs34532503	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34662965	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34929849	0.91[EUR][1000 genomes]
rs35011964	0.88[EUR][1000 genomes]
rs35561856	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35859241	0.97[AMR][1000 genomes]
rs3736484	0.96[ASN][1000 genomes]
rs4465557	0.83[EUR][1000 genomes]
rs4774594	0.87[EUR][1000 genomes]
rs4775954	0.85[EUR][1000 genomes]
rs55725532	0.90[EUR][1000 genomes]
rs55803403	0.93[ASN][1000 genomes]
rs56127635	0.89[ASN][1000 genomes]
rs57860217	0.93[ASN][1000 genomes]
rs61618680	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61642433	0.84[ASN][1000 genomes]
rs6493507	0.85[EUR][1000 genomes]
rs6493511	0.86[EUR][1000 genomes]
rs6493512	0.86[EUR][1000 genomes]
rs6493514	0.86[EUR][1000 genomes]
rs7180329	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73399525	1.00[ASN][1000 genomes]
rs74013220	1.00[ASN][1000 genomes]
rs74013290	0.85[ASN][1000 genomes]
rs8026587	0.86[AMR][1000 genomes]
rs8032454	0.80[ASN][1000 genomes]
rs8032713	0.96[ASN][1000 genomes]
rs8038520	1.00[ASN][1000 genomes]
rs956171	0.85[EUR][1000 genomes]
rs977137	0.96[ASN][1000 genomes]
rs9806124	1.00[ASN][1000 genomes]
rs9944266	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv904216	chr15:51631479-51739808	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv904217	chr15:51695653-51881980	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51707200-51738800	Weak transcription	Placenta	Placenta
2	chr15:51707400-51740200	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:51731000-51740600	Weak transcription	Brain Substantia Nigra	brain
4	chr15:51731200-51738600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:51732000-51740600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:51732800-51738600	Weak transcription	Brain Angular Gyrus	brain
7	chr15:51732800-51740200	Weak transcription	K562	blood
8	chr15:51733000-51740600	Weak transcription	Brain Anterior Caudate	brain
9	chr15:51733800-51740000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:51734000-51740600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:51734600-51739000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:51734600-51748800	Weak transcription	Fetal Intestine Small	intestine
13	chr15:51734800-51737800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:51734800-51740600	Weak transcription	Lung	lung
15	chr15:51735000-51739400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:51735200-51738600	Weak transcription	Adipose Nuclei	Adipose
17	chr15:51735200-51742000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:51735400-51739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:51735400-51741200	Weak transcription	Brain Germinal Matrix	brain
20	chr15:51735600-51738800	Weak transcription	Aorta	Aorta
21	chr15:51735600-51739600	Weak transcription	HSMM	muscle
22	chr15:51735600-51741000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:51735800-51740600	Weak transcription	Spleen	Spleen
24	chr15:51735800-51742000	Weak transcription	Fetal Kidney	kidney
25	chr15:51736000-51738600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:51736000-51741200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:51736200-51740600	Weak transcription	Fetal Stomach	stomach
28	chr15:51736400-51738000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:51736400-51738600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:51736400-51739400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr15:51736600-51738000	Weak transcription	GM12878-XiMat	blood
32	chr15:51736600-51741400	Weak transcription	Fetal Thymus	thymus
33	chr15:51736800-51751200	Weak transcription	HUVEC	blood vessel
34	chr15:51737000-51738600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:51737000-51738800	Weak transcription	Fetal Intestine Large	intestine
36	chr15:51737000-51739200	Weak transcription	Fetal Brain Female	brain
37	chr15:51737000-51740600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:51737000-51775600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr15:51737000-51776400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:51737200-51738000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:51737200-51738600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:51737200-51738800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:51737200-51738800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:51737200-51739600	Strong transcription	A549	lung
45	chr15:51737200-51741600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:51737400-51738600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:51737400-51738800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:51737400-51739000	Weak transcription	Liver	Liver
49	chr15:51737400-51740600	Weak transcription	Primary T cells from cord blood	blood
50	chr15:51737400-51740600	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links