Variant report

Variant	rs2122278
Chromosome Location	chr13:49349906-49349907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49348522..49350092-chr13:49351651..49354289,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10220140	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12100214	0.92[EUR][1000 genomes]
rs12429439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1536136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1597325	0.83[ASN][1000 genomes]
rs17072247	0.89[ASN][1000 genomes]
rs1868550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561479	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs732769	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7329905	0.83[ASN][1000 genomes]
rs7334792	0.85[ASN][1000 genomes]
rs7337637	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73480227	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7989311	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7999498	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8000501	0.92[EUR][1000 genomes]
rs959353	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9595988	0.87[ASN][1000 genomes]
rs9595995	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9595997	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9596011	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2758327	chr13:49283983-49472517	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2759936	chr13:49283983-49472517	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1044086	chr13:49331713-49350131	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49346400-49350600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr13:49346600-49357200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:49346800-49352200	Weak transcription	Left Ventricle	heart
4	chr13:49347400-49352000	Enhancers	Hela-S3	cervix
5	chr13:49347800-49352000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr13:49348400-49350000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:49348400-49351400	Weak transcription	Placenta	Placenta
8	chr13:49349200-49351000	Enhancers	NH-A	brain
9	chr13:49349200-49351400	Enhancers	NHLF	lung
10	chr13:49349200-49356800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:49349400-49350000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:49349600-49350600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr13:49349600-49350600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:49349600-49351200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr13:49349600-49351200	Enhancers	HSMM	muscle
16	chr13:49349600-49351400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:49349800-49350000	Flanking Active TSS	NHDF-Ad	bronchial
18	chr13:49349800-49350400	Flanking Active TSS	Osteobl	bone
19	chr13:49349800-49350600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:49349800-49351000	Enhancers	HMEC	breast
21	chr13:49349800-49351000	Enhancers	HSMMtube	muscle
22	chr13:49349800-49351200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links