Variant report

Variant	rs1669858
Chromosome Location	chr15:52708189-52708190
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	chr15:52701268..52703457-chr15:52706501..52708965,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1001522	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10083671	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10083673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1009157	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs10467925	0.83[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs10518687	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1125460	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12324100	0.88[CEU][hapmap]
rs12324121	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs12898655	0.97[ASN][1000 genomes]
rs12909874	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914979	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1464963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669856	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669867	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1724589	0.89[AFR][1000 genomes]
rs1724591	0.92[AFR][1000 genomes]
rs1724628	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724629	0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724631	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724634	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724639	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1724641	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17542017	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242057	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2242058	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2414150	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2414151	0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2444013	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2950056	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs35134548	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35523401	0.94[ASN][1000 genomes]
rs3858907	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280181	0.88[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap]
rs4519295	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4776039	0.83[ASN][1000 genomes]
rs4776046	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62015999	0.84[ASN][1000 genomes]
rs62023267	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71474804	0.92[ASN][1000 genomes]
rs7176061	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7176482	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7176639	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7182150	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs722436	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs752864	0.91[CHB][hapmap]
rs752865	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs752866	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs8028033	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8033626	0.83[ASN][1000 genomes]
rs935892	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1669858	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs1669858	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
2	chr15:52663200-52711400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:52663400-52708600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
5	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
6	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:52676400-52709800	Weak transcription	NHLF	lung
8	chr15:52676400-52721400	Weak transcription	Gastric	stomach
9	chr15:52676600-52718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
13	chr15:52680600-52719800	Weak transcription	NH-A	brain
14	chr15:52680800-52716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:52680800-52730000	Weak transcription	Brain Angular Gyrus	brain
16	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
17	chr15:52684000-52719800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:52684800-52719800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:52684800-52730000	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:52685000-52717000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:52685400-52711000	Weak transcription	NHDF-Ad	bronchial
22	chr15:52685400-52730000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:52687000-52714800	Weak transcription	Psoas Muscle	Psoas
24	chr15:52687000-52715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:52689600-52730200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:52689600-52730200	Weak transcription	Left Ventricle	heart
27	chr15:52689600-52730400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:52696000-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr15:52696200-52719800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:52697000-52709800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr15:52697200-52715000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:52697200-52718400	Weak transcription	Dnd41	blood
33	chr15:52697200-52720000	Weak transcription	Ovary	ovary
34	chr15:52697200-52730000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr15:52697200-52730400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:52697200-52738600	Weak transcription	Fetal Brain Female	brain
37	chr15:52697400-52720000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:52697400-52730400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:52697600-52708400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:52697600-52709400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr15:52697600-52710200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:52697600-52720600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:52697800-52709400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:52697800-52709800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:52697800-52715800	Weak transcription	Adipose Nuclei	Adipose
46	chr15:52698600-52720400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:52699000-52709000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:52699400-52710200	Strong transcription	Primary B cells from cord blood	blood
49	chr15:52699600-52710000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:52701400-52713000	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links