Variant report

Variant	rs28496515
Chromosome Location	chr3:50595480-50595481
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50594854..50596766-chr3:50606531..50608188,2	MCF-7	breast:
2	chr3:50483163..50485721-chr3:50593817..50596620,2	MCF-7	breast:
3	chr3:50594685..50598509-chr3:50599030..50605276,6	K562	blood:
4	chr3:50593486..50596662-chr3:50604941..50607206,3	MCF-7	breast:
5	chr3:50595096..50597845-chr3:50598806..50601050,2	MCF-7	breast:
6	chr3:50587657..50590560-chr3:50595008..50597465,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114735	Chromatin interaction
ENSG00000088543	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13321914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050997	1.00[AMR][1000 genomes]
rs17051020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051027	1.00[AMR][1000 genomes]
rs17051036	1.00[AMR][1000 genomes]
rs17051472	1.00[AMR][1000 genomes]
rs2085581	1.00[AMR][1000 genomes]
rs2232249	1.00[AMR][1000 genomes]
rs2232252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2355324	1.00[AMR][1000 genomes]
rs28525150	1.00[AMR][1000 genomes]
rs28546448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs736472	1.00[AMR][1000 genomes]
rs751850	1.00[AMR][1000 genomes]
rs762893	1.00[AMR][1000 genomes]
rs762894	1.00[AMR][1000 genomes]
rs9822071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9832171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9850032	1.00[AMR][1000 genomes]
rs9866852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh 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	27 gene(s)	inside rSNPs	diseases
11	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50578600-50595800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:50583600-50603400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:50586000-50597200	Weak transcription	Right Atrium	heart
4	chr3:50587600-50603800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:50588400-50603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:50589600-50604000	Weak transcription	Fetal Lung	lung
7	chr3:50589800-50595600	Weak transcription	Fetal Stomach	stomach
8	chr3:50592200-50596400	Enhancers	Fetal Muscle Leg	muscle
9	chr3:50592600-50597200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:50592800-50604000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:50593200-50596000	Weak transcription	Ovary	ovary
12	chr3:50593200-50597000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:50593400-50601400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:50593400-50602800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:50593600-50604000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:50593800-50596000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:50593800-50604200	Weak transcription	Brain Germinal Matrix	brain
18	chr3:50594000-50595800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:50594200-50596000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:50594200-50596400	Enhancers	Fetal Heart	heart
21	chr3:50594200-50596400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:50594200-50604000	Weak transcription	Pancreas	Pancrea
23	chr3:50594400-50595800	Enhancers	Right Ventricle	heart
24	chr3:50594600-50596200	Weak transcription	Brain Angular Gyrus	brain
25	chr3:50594600-50597400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:50594600-50604000	Weak transcription	Brain Substantia Nigra	brain
27	chr3:50594800-50601000	Weak transcription	Fetal Brain Female	brain
28	chr3:50594800-50604000	Weak transcription	Adipose Nuclei	Adipose
29	chr3:50595000-50595800	Enhancers	Fetal Thymus	thymus
30	chr3:50595200-50595800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:50595200-50595800	Enhancers	Left Ventricle	heart
32	chr3:50595400-50596000	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links