Variant report

Variant	rs13059155
Chromosome Location	chr3:23430434-23430435
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	chr3:23429124..23431176-chr3:23435283..23438143,3	MCF-7	breast:

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs12106681	0.88[EUR][1000 genomes]
rs13059557	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13060251	0.88[EUR][1000 genomes]
rs13063183	0.81[AFR][1000 genomes]
rs13063451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13065375	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13065646	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13066741	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13070136	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13070865	0.86[AFR][1000 genomes]
rs13071171	0.97[EUR][1000 genomes]
rs13072325	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13073761	0.97[EUR][1000 genomes]
rs13076412	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13076527	0.97[EUR][1000 genomes]
rs13078970	0.88[EUR][1000 genomes]
rs13082311	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13084870	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13085173	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13085266	0.97[EUR][1000 genomes]
rs13087238	0.94[EUR][1000 genomes]
rs13087563	0.88[EUR][1000 genomes]
rs13088756	0.98[EUR][1000 genomes]
rs13090125	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13090303	0.86[AFR][1000 genomes]
rs13090335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13090633	0.86[EUR][1000 genomes]
rs13091625	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13091634	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13092830	0.89[EUR][1000 genomes]
rs13095736	0.86[AFR][1000 genomes]
rs13095737	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13096187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13098798	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13100499	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13100605	0.88[EUR][1000 genomes]
rs34134134	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34171096	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34225647	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34322396	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34443476	0.89[EUR][1000 genomes]
rs34474714	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34504120	0.88[EUR][1000 genomes]
rs34584255	0.88[EUR][1000 genomes]
rs34619482	0.97[EUR][1000 genomes]
rs34732257	0.97[EUR][1000 genomes]
rs34743949	0.91[EUR][1000 genomes]
rs34758087	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34804976	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34827773	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34894979	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34916096	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34916962	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34928302	0.86[AFR][1000 genomes]
rs34928966	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35021696	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35027557	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35028631	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35038414	0.81[AFR][1000 genomes]
rs35055753	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35096750	0.88[EUR][1000 genomes]
rs35098118	0.81[AFR][1000 genomes]
rs35105861	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35121170	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35152860	0.97[EUR][1000 genomes]
rs35156003	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35177750	0.98[EUR][1000 genomes]
rs35179250	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35190363	0.97[EUR][1000 genomes]
rs35209889	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35218978	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35230557	0.97[EUR][1000 genomes]
rs35240920	0.88[EUR][1000 genomes]
rs35245309	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35266274	0.86[EUR][1000 genomes]
rs35273607	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35314441	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35320722	0.86[AFR][1000 genomes]
rs35346188	0.88[EUR][1000 genomes]
rs35347265	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35383024	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35402533	0.91[EUR][1000 genomes]
rs35408638	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35497505	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35587590	0.88[EUR][1000 genomes]
rs35649850	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35657558	0.91[EUR][1000 genomes]
rs35776486	0.88[EUR][1000 genomes]
rs35778452	0.98[EUR][1000 genomes]
rs35869522	0.91[EUR][1000 genomes]
rs35902312	0.97[EUR][1000 genomes]
rs35907941	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35928592	0.97[EUR][1000 genomes]
rs35975795	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36021750	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36082634	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36123653	0.86[AFR][1000 genomes]
rs36123979	0.88[EUR][1000 genomes]
rs36124326	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36183485	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58522464	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60074421	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71317827	0.88[EUR][1000 genomes]
rs71317829	0.88[EUR][1000 genomes]
rs71317834	0.83[EUR][1000 genomes]
rs71322171	0.91[EUR][1000 genomes]
rs71322172	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71322173	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71322174	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71322180	0.86[AFR][1000 genomes]
rs71322181	0.86[AFR][1000 genomes]
rs71322183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71322184	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71322185	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71322187	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71322189	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71322190	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71322195	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71322200	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv876624	chr3:23385877-23483536	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1012236	chr3:23408427-23469063	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1010032	chr3:23408985-23469063	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23409200-23431800	Weak transcription	Aorta	Aorta
2	chr3:23420000-23433600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:23425800-23432200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:23427000-23445000	Weak transcription	Right Ventricle	heart
5	chr3:23427600-23432000	Enhancers	Primary B cells from cord blood	blood
6	chr3:23428000-23431600	Weak transcription	Psoas Muscle	Psoas
7	chr3:23428000-23431800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:23428400-23431400	Active TSS	Duodenum Mucosa	Duodenum
9	chr3:23428400-23431400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr3:23428600-23435400	Weak transcription	Brain Substantia Nigra	brain
11	chr3:23428800-23430600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:23429200-23431000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:23429400-23430600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:23429600-23430600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:23429600-23430600	Weak transcription	GM12878-XiMat	blood
16	chr3:23429600-23430800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:23429600-23430800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:23429800-23431000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:23429800-23432200	Weak transcription	Liver	Liver
20	chr3:23429800-23445400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:23430000-23432200	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:23430200-23430600	Weak transcription	Fetal Heart	heart
23	chr3:23430200-23431000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:23430400-23431000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:23430400-23431400	Enhancers	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links