Variant report

Variant	rs28493625
Chromosome Location	chr3:78985640-78985641
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	chr3:78979408..78982289-chr3:78984181..78986172,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1031933	0.95[ASN][1000 genomes]
rs10514741	0.95[ASN][1000 genomes]
rs12330873	1.00[EUR][1000 genomes]
rs13321792	0.95[ASN][1000 genomes]
rs17016646	0.95[ASN][1000 genomes]
rs17016648	0.95[ASN][1000 genomes]
rs17016656	0.95[ASN][1000 genomes]
rs28722753	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729472	0.95[ASN][1000 genomes]
rs57432814	0.95[ASN][1000 genomes]
rs58249522	0.95[ASN][1000 genomes]
rs61270372	1.00[EUR][1000 genomes]
rs61490942	1.00[EUR][1000 genomes]
rs6788270	1.00[EUR][1000 genomes]
rs72894482	1.00[EUR][1000 genomes]
rs72894501	1.00[EUR][1000 genomes]
rs72896405	1.00[EUR][1000 genomes]
rs72896408	1.00[EUR][1000 genomes]
rs72896421	1.00[EUR][1000 genomes]
rs72896425	1.00[EUR][1000 genomes]
rs72896439	1.00[EUR][1000 genomes]
rs72896443	1.00[EUR][1000 genomes]
rs72896444	1.00[EUR][1000 genomes]
rs72896497	1.00[EUR][1000 genomes]
rs72904252	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72904254	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72904257	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72904261	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72906145	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72906180	0.95[ASN][1000 genomes]
rs72910208	0.95[ASN][1000 genomes]
rs72910211	0.95[ASN][1000 genomes]
rs72910220	0.95[ASN][1000 genomes]
rs9808917	1.00[EUR][1000 genomes]
rs9813971	1.00[EUR][1000 genomes]
rs9817408	1.00[EUR][1000 genomes]
rs9818374	1.00[EUR][1000 genomes]
rs9831603	1.00[EUR][1000 genomes]
rs9832632	0.95[ASN][1000 genomes]
rs9833345	0.95[ASN][1000 genomes]
rs9845223	0.95[ASN][1000 genomes]
rs9847098	1.00[EUR][1000 genomes]
rs9853126	0.95[ASN][1000 genomes]
rs9858080	0.95[ASN][1000 genomes]
rs9861490	0.95[ASN][1000 genomes]
rs9870336	0.95[ASN][1000 genomes]
rs9872429	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9876641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78959600-78987200	Weak transcription	Fetal Lung	lung
2	chr3:78963200-78991000	Weak transcription	Fetal Brain Male	brain
3	chr3:78967200-78987200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:78967200-79000600	Weak transcription	Fetal Kidney	kidney
5	chr3:78968800-78987200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:78969000-78990800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:78969000-78991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:78969200-78990400	Weak transcription	NHEK	skin
9	chr3:78969600-79000600	Weak transcription	HepG2	liver
10	chr3:78970400-78991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:78975600-78987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:78977200-78990800	Weak transcription	Psoas Muscle	Psoas
13	chr3:78977400-78987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:78977400-78987200	Weak transcription	Fetal Stomach	stomach
15	chr3:78978400-78992200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:78978800-78990800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:78979600-78987000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:78979600-78987200	Weak transcription	Aorta	Aorta
19	chr3:78980600-78989400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:78981600-78991600	Weak transcription	Fetal Heart	heart
21	chr3:78982400-79001800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:78982800-78987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:78983800-78989200	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:78984400-78990200	Weak transcription	Osteobl	bone
25	chr3:78985000-78987200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:78985200-78989200	Weak transcription	Brain Substantia Nigra	brain
27	chr3:78985400-78987200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:78985600-78987200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links