Variant report

Variant	rs13392080
Chromosome Location	chr2:189299121-189299122
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	chr2:189159168..189161448-chr2:189298953..189301170,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10153666	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10153862	1.00[AMR][1000 genomes]
rs10171583	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10174521	1.00[AMR][1000 genomes]
rs10184797	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10185493	0.98[AFR][1000 genomes]
rs10188279	0.90[YRI][hapmap]
rs10190081	0.84[AFR][1000 genomes]
rs10190630	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10192679	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10197598	0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10198965	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10199401	0.90[AFR][1000 genomes]
rs10207510	0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10211425	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10211482	1.00[AMR][1000 genomes]
rs10439261	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11904835	1.00[AMR][1000 genomes]
rs13386579	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13390367	1.00[AMR][1000 genomes]
rs13391799	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13391898	0.85[AFR][1000 genomes]
rs13393442	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs13399616	0.83[YRI][hapmap]
rs13399903	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401242	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401321	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401975	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13402240	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13403508	1.00[MEX][hapmap];0.94[MKK][hapmap]
rs13403672	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13404901	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411351	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13414813	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418323	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13423468	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13424443	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28528331	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4667232	1.00[AMR][1000 genomes]
rs59080597	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6434282	0.83[YRI][hapmap]
rs6434283	0.83[YRI][hapmap]
rs6434287	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs6705869	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6710795	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6742748	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6744742	0.83[YRI][hapmap]
rs6748075	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6755644	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6759147	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs6761280	1.00[AMR][1000 genomes]
rs7423329	1.00[MEX][hapmap]
rs7423378	1.00[MEX][hapmap]
rs7579593	1.00[MEX][hapmap]
rs7589600	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7593824	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs9288154	0.82[AFR][1000 genomes]
rs9288156	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv533786	chr2:189248503-189354495	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13392080	FERMT2	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189285600-189318800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:189285800-189318200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:189292400-189306200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:189293600-189308800	Weak transcription	HUVEC	blood vessel
5	chr2:189294200-189308000	Weak transcription	Ovary	ovary
6	chr2:189295600-189304200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:189297200-189299200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr2:189297400-189299200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:189297800-189299200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr2:189297800-189303800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:189298600-189304000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:189298800-189299800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:189298800-189303200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:189299000-189303400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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