Variant report

Variant	rs12638283
Chromosome Location	chr3:145617310-145617311
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	chr3:145604775..145606383-chr3:145616815..145618517,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10513264	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12495853	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1398778	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1398780	0.95[AFR][1000 genomes]
rs1502972	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1502973	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1513398	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708436	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1849514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949222	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1996114	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2055994	0.87[ASN][1000 genomes]
rs2174093	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2202232	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs512600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440396	0.94[ASN][1000 genomes]
rs6440397	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440400	0.94[AFR][1000 genomes]
rs669904	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762748	0.98[AFR][1000 genomes]
rs6789220	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808863	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7620607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635162	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7638287	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7639600	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641056	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641060	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs905415	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs905417	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs905418	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs924690	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289704	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9828083	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9828457	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850303	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9850618	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9850800	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9860922	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9880600	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv3379945	chr3:145351163-145679850	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv877610	chr3:145465395-145653627	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2751980	chr3:145473020-145758194	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1013475	chr3:145478985-145750509	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1010509	chr3:145478985-145757483	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1005624	chr3:145486437-145750509	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv999344	chr3:145506353-145750883	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv536757	chr3:145506353-145750883	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv33307	chr3:145506383-145667833	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv877611	chr3:145525989-145653627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv877612	chr3:145542558-145653627	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
14	esv2757015	chr3:145615852-145661771	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv2759186	chr3:145615852-145661771	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145615000-145621000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:145615800-145617400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr3:145615800-145617400	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr3:145616000-145617600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:145616600-145617400	Enhancers	HSMMtube	muscle
6	chr3:145616600-145618200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:145616600-145621000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:145617000-145617400	Enhancers	Hela-S3	cervix
9	chr3:145617000-145617600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:145617200-145617400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr3:145617200-145617600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links