Variant report

Variant	rs2950056
Chromosome Location	chr15:52733671-52733672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52732225..52734502-chr15:52735586..52737887,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1001522	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs10083671	0.88[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs10083673	0.85[GIH][hapmap]
rs1009157	0.81[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]
rs10518687	0.89[GIH][hapmap]
rs12324100	0.89[GIH][hapmap]
rs12324121	0.87[GIH][hapmap]
rs12898655	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1464963	0.85[GIH][hapmap]
rs1464964	0.92[AFR][1000 genomes]
rs1669856	0.90[AFR][1000 genomes]
rs1669858	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1669867	0.88[ASW][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs1693490	0.84[LWK][hapmap]
rs1724589	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1724591	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1724628	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1724629	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1724631	0.82[ASW][hapmap];0.84[GIH][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1724634	0.88[AFR][1000 genomes]
rs1724639	0.85[AFR][1000 genomes]
rs1724641	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2242057	0.82[CHD][hapmap];0.89[GIH][hapmap]
rs2242058	0.82[CHD][hapmap];0.89[GIH][hapmap]
rs2414151	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2444013	0.92[AFR][1000 genomes]
rs35523401	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3858907	0.92[AFR][1000 genomes]
rs71474804	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7176061	0.96[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7176482	0.87[GIH][hapmap]
rs7176639	0.89[GIH][hapmap]
rs722436	0.92[AFR][1000 genomes]
rs8028033	0.82[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap]
rs935892	1.00[YRI][hapmap];0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2950056	MYO5A	cis	cerebellum	SCAN
rs2950056	SPPL2A	cis	parietal	SCAN
rs2950056	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs2950056	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
2	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
3	chr15:52697200-52738600	Weak transcription	Fetal Brain Female	brain
4	chr15:52702400-52737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:52721400-52737800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr15:52721400-52739000	Weak transcription	Primary B cells from cord blood	blood
7	chr15:52728600-52737400	Weak transcription	Psoas Muscle	Psoas
8	chr15:52729000-52739400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr15:52729200-52734800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:52729800-52734800	Enhancers	Adipose Nuclei	Adipose
11	chr15:52730000-52734200	Enhancers	Brain Cingulate Gyrus	brain
12	chr15:52730000-52735600	Enhancers	Brain Anterior Caudate	brain
13	chr15:52730200-52734800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:52730400-52744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:52730600-52734200	Weak transcription	GM12878-XiMat	blood
16	chr15:52730600-52734400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:52730600-52736200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr15:52730600-52737200	Weak transcription	Right Ventricle	heart
19	chr15:52730600-52739400	Weak transcription	Esophagus	oesophagus
20	chr15:52730600-52741600	Weak transcription	Ovary	ovary
21	chr15:52730600-52741600	Weak transcription	HUVEC	blood vessel
22	chr15:52730600-52741800	Weak transcription	Gastric	stomach
23	chr15:52730800-52734200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:52730800-52735400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr15:52730800-52738000	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:52730800-52741800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr15:52731200-52733800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:52731200-52734400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:52731200-52734400	Weak transcription	Right Atrium	heart
30	chr15:52731600-52734400	Enhancers	Brain Angular Gyrus	brain
31	chr15:52731600-52734400	Enhancers	Brain Hippocampus Middle	brain
32	chr15:52731800-52734600	Enhancers	HMEC	breast
33	chr15:52731800-52734800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr15:52732200-52734600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr15:52732200-52734600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:52732200-52734600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:52732200-52734800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:52732200-52734800	Enhancers	A549	lung
39	chr15:52732200-52734800	Enhancers	HSMM	muscle
40	chr15:52732200-52734800	Enhancers	HSMMtube	muscle
41	chr15:52732200-52734800	Enhancers	NHEK	skin
42	chr15:52732400-52733800	Enhancers	NHDF-Ad	bronchial
43	chr15:52732400-52734200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:52732400-52734600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:52732400-52737200	Weak transcription	Left Ventricle	heart
46	chr15:52732600-52734000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:52732600-52734400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:52732600-52737200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr15:52732600-52750600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:52732800-52733800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links