Variant report

Variant	rs9301920
Chromosome Location	chr13:94624463-94624464
allele	C/T
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: 85 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10492635	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap]
rs1318496	0.89[CHB][hapmap];0.90[CHD][hapmap]
rs1337835	1.00[YRI][hapmap]
rs1415736	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs1415737	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1415740	1.00[CEU][hapmap];0.81[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415741	1.00[EUR][1000 genomes]
rs1415742	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1415743	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs1556082	0.82[CEU][hapmap]
rs17253537	0.82[CEU][hapmap]
rs1832360	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1933145	0.88[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1933146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1933147	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1933148	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389078	0.86[AMR][1000 genomes]
rs2892675	0.84[CEU][hapmap];0.86[AMR][1000 genomes]
rs35534726	0.92[EUR][1000 genomes]
rs3904817	0.94[EUR][1000 genomes]
rs4528446	1.00[EUR][1000 genomes]
rs4771884	0.95[EUR][1000 genomes]
rs4771885	0.84[AMR][1000 genomes]
rs6492685	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs6650320	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs6650321	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7323264	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7325794	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7327560	0.95[EUR][1000 genomes]
rs7985851	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7994682	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap]
rs8000417	0.84[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes]
rs928188	0.91[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs9284275	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9284276	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9301919	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301921	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs9301926	0.82[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap]
rs945937	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945938	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9516319	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9516322	0.93[EUR][1000 genomes]
rs9516323	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516324	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516325	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs9516331	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9524284	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9524287	0.91[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs9524288	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524290	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524291	0.95[EUR][1000 genomes]
rs9524292	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9524293	0.91[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs9524294	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524295	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524297	0.94[EUR][1000 genomes]
rs9524298	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs9524299	0.91[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs9524300	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524302	0.82[CEU][hapmap]
rs9524306	0.82[CEU][hapmap]
rs9524309	0.85[CEU][hapmap]
rs9524311	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs9524312	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9524313	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs9524314	0.82[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap]
rs9524316	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9524318	0.81[CHB][hapmap]
rs9524319	0.82[CEU][hapmap]
rs9584175	0.94[EUR][1000 genomes]
rs9584176	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9589877	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9589880	0.89[CHB][hapmap]
rs9589881	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs9589882	0.82[CEU][hapmap];0.80[CHB][hapmap]
rs9589883	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs9589884	0.87[ASN][1000 genomes]
rs981341	0.84[AMR][1000 genomes];0.94[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
rs9301920	CCL23	trans	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94618200-94633800	Weak transcription	Fetal Stomach	stomach
2	chr13:94623000-94631400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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