Variant report

Variant	rs13189127
Chromosome Location	chr5:58707941-58707942
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs11951025	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11959801	0.88[CEU][hapmap]
rs11960438	0.87[CEU][hapmap]
rs12186492	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186633	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187142	0.90[EUR][1000 genomes]
rs12187317	0.88[EUR][1000 genomes]
rs12187338	0.90[EUR][1000 genomes]
rs12188859	0.90[EUR][1000 genomes]
rs13154145	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159276	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162275	0.93[EUR][1000 genomes]
rs13184036	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13189436	0.88[EUR][1000 genomes]
rs13189942	0.89[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348709	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs1348710	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs1457145	0.88[CEU][hapmap]
rs1541672	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs1541673	0.93[EUR][1000 genomes]
rs1579845	0.93[EUR][1000 genomes]
rs1579846	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889805	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs16889810	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs17725949	0.88[CEU][hapmap]
rs17726292	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782969	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971061	0.93[EUR][1000 genomes]
rs1975533	0.91[EUR][1000 genomes]
rs28696115	0.90[EUR][1000 genomes]
rs2898243	0.88[EUR][1000 genomes]
rs34084254	0.93[EUR][1000 genomes]
rs34118182	0.90[EUR][1000 genomes]
rs34433570	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34468745	0.91[EUR][1000 genomes]
rs34624326	0.93[EUR][1000 genomes]
rs34733788	0.93[EUR][1000 genomes]
rs34797165	0.93[EUR][1000 genomes]
rs34873866	0.93[EUR][1000 genomes]
rs35643183	0.90[EUR][1000 genomes]
rs62357468	0.90[EUR][1000 genomes]
rs62357478	0.93[EUR][1000 genomes]
rs62357496	0.94[EUR][1000 genomes]
rs62357500	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62358055	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861992	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs6869578	0.93[EUR][1000 genomes]
rs6870927	0.93[EUR][1000 genomes]
rs6871410	0.93[EUR][1000 genomes]
rs6872134	1.00[YRI][hapmap]
rs6874460	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs6874473	0.93[EUR][1000 genomes]
rs6875027	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs6875497	0.93[EUR][1000 genomes]
rs6876934	0.93[EUR][1000 genomes]
rs6879216	0.93[EUR][1000 genomes]
rs6879510	0.93[EUR][1000 genomes]
rs6879949	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs6883834	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs6885690	0.93[EUR][1000 genomes]
rs6887017	1.00[YRI][hapmap]
rs6888059	0.90[EUR][1000 genomes]
rs6891589	0.93[EUR][1000 genomes]
rs6892252	0.93[EUR][1000 genomes]
rs6892879	0.93[EUR][1000 genomes]
rs6893655	0.93[EUR][1000 genomes]
rs6893668	0.93[EUR][1000 genomes]
rs6893986	0.93[EUR][1000 genomes]
rs6895550	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs6896519	0.90[EUR][1000 genomes]
rs6897015	0.85[CEU][hapmap]
rs7701455	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs7735228	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs7735376	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs7735572	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9918215	0.93[EUR][1000 genomes]
rs9918225	0.90[EUR][1000 genomes]
rs9918228	0.89[CEU][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv881705	chr5:58668669-58745872	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1034656	chr5:58674724-58755580	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv598253	chr5:58675538-58754510	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58682000-58711800	Weak transcription	Psoas Muscle	Psoas
2	chr5:58704200-58714200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:58704600-58708400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:58704600-58712000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:58704600-58712200	Weak transcription	Fetal Lung	lung
6	chr5:58704800-58711600	Weak transcription	Fetal Stomach	stomach
7	chr5:58705600-58710000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:58705600-58751400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:58706400-58709800	Strong transcription	A549	lung
10	chr5:58707600-58714800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links