Variant report

Variant	rs9524293
Chromosome Location	chr13:94623096-94623097
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	chr13:94618671..94621851-chr13:94622877..94625492,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1318496	0.81[CEU][hapmap]
rs1415736	0.80[TSI][hapmap]
rs1415740	0.88[CEU][hapmap];0.96[EUR][1000 genomes]
rs1415741	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1415742	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1832360	1.00[EUR][1000 genomes]
rs1933145	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1933146	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs1933147	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs1933148	0.95[EUR][1000 genomes]
rs2021983	0.81[CEU][hapmap]
rs35534726	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3904817	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4528446	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4771884	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6492685	0.81[CEU][hapmap]
rs6650320	0.91[CEU][hapmap]
rs6650321	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs72644500	0.93[ASN][1000 genomes]
rs7323264	0.91[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs7325794	0.91[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7327560	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7985851	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs928188	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9284275	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs9284276	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs9301919	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9301920	0.91[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs9301921	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs945937	0.96[EUR][1000 genomes]
rs945938	0.94[EUR][1000 genomes]
rs9516319	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs9516322	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9516323	1.00[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9516324	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9516325	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9516330	0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs9524284	0.91[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9524287	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524288	1.00[EUR][1000 genomes]
rs9524290	1.00[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs9524291	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524292	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs9524294	0.96[EUR][1000 genomes]
rs9524295	0.94[EUR][1000 genomes]
rs9524297	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9524298	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9524299	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9524300	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs9524302	0.92[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs9524303	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs9524304	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs9524305	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap]
rs9524306	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs9524309	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs9524310	0.93[ASN][1000 genomes]
rs9561490	0.81[CEU][hapmap]
rs9561491	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs9584175	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9584176	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9589877	1.00[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9589878	0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs9589880	0.81[CEU][hapmap]
rs9589881	0.81[CEU][hapmap]
rs981341	0.90[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	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv933807	chr13:94187158-94845505	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1045230	chr13:94277683-94764671	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916640	chr13:94521959-95101443	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv533063	chr13:94560362-95101443	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1052141	chr13:94596760-94689892	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9524293	CCL23	trans	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94618200-94633800	Weak transcription	Fetal Stomach	stomach
2	chr13:94620200-94623800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr13:94623000-94624000	Weak transcription	Fetal Lung	lung
4	chr13:94623000-94631400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links