Variant report

Variant	rs9524299
Chromosome Location	chr13:94633244-94633245
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];0.94[EUR][1000 genomes]
rs1415741	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415742	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1832360	0.98[EUR][1000 genomes]
rs1933145	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1933146	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs1933147	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs1933148	0.93[EUR][1000 genomes]
rs2021983	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs35534726	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3904817	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4528446	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4771884	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492685	0.81[CEU][hapmap]
rs6650320	0.91[CEU][hapmap]
rs6650321	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs72644500	0.96[ASN][1000 genomes]
rs7323264	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs7325794	0.91[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7327560	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7985851	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs928188	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9284275	1.00[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9284276	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs9301919	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs9301920	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs9301921	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945937	0.94[EUR][1000 genomes]
rs945938	0.93[EUR][1000 genomes]
rs9516319	1.00[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9516322	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9516323	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs9516324	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9516325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516330	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9524284	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524287	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524288	0.98[EUR][1000 genomes]
rs9524290	1.00[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs9524291	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9524292	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs9524293	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]
rs9524294	0.94[EUR][1000 genomes]
rs9524295	0.96[EUR][1000 genomes]
rs9524297	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524300	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9524302	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9524303	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9524304	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9524305	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9524306	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9524309	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs9524310	0.97[ASN][1000 genomes]
rs9561490	0.81[CEU][hapmap]
rs9561491	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs9584175	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9584176	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9589877	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs9589878	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9589880	0.81[CEU][hapmap]
rs9589881	0.81[CEU][hapmap]
rs981341	0.89[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
rs9524299	CCL23	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94618200-94633800	Weak transcription	Fetal Stomach	stomach
2	chr13:94632600-94634000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr13:94633000-94635000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr13:94633000-94635800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr13:94633200-94634200	Weak transcription	Colon Smooth Muscle	Colon

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