Variant report

Variant	rs6992829
Chromosome Location	chr8:52189796-52189797
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	chr8:52189412..52191198-chr8:52195033..52197163,2	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1003095	0.85[CEU][hapmap]
rs10091279	0.85[CEU][hapmap]
rs10101803	0.85[CEU][hapmap]
rs1017352	0.85[CEU][hapmap]
rs1017353	0.85[CEU][hapmap]
rs1017354	0.85[CEU][hapmap]
rs1052704	0.90[CEU][hapmap]
rs10958261	0.90[CEU][hapmap]
rs1219677	0.85[CEU][hapmap]
rs1219680	0.85[CEU][hapmap]
rs1236097	0.85[CEU][hapmap]
rs12550267	0.89[CEU][hapmap]
rs1346954	0.85[CEU][hapmap]
rs1370445	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs1370446	0.90[CEU][hapmap];0.90[MEX][hapmap]
rs1431619	0.85[CEU][hapmap]
rs1431620	0.85[CEU][hapmap]
rs1431623	0.83[CEU][hapmap]
rs1431624	0.82[CEU][hapmap]
rs1431625	0.85[CEU][hapmap]
rs1431626	0.85[CEU][hapmap]
rs1431627	0.85[CEU][hapmap]
rs1431628	0.85[CEU][hapmap]
rs1437593	0.85[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs1560508	0.85[CEU][hapmap]
rs1560509	0.85[CEU][hapmap]
rs1560510	0.85[CEU][hapmap]
rs17261657	0.80[CEU][hapmap]
rs1816630	0.90[CEU][hapmap]
rs1991691	0.85[CEU][hapmap]
rs1991692	0.85[CEU][hapmap]
rs2217988	0.85[CEU][hapmap]
rs2915454	0.85[CEU][hapmap]
rs2915457	0.85[CEU][hapmap]
rs2915460	0.85[CEU][hapmap]
rs2915461	0.85[CEU][hapmap]
rs2915465	0.85[CEU][hapmap]
rs2915467	0.89[CEU][hapmap]
rs2915468	0.85[CEU][hapmap]
rs2915469	0.85[CEU][hapmap]
rs2915471	0.83[CEU][hapmap]
rs2915473	0.85[CEU][hapmap]
rs2915475	0.85[CEU][hapmap]
rs2915476	0.85[CEU][hapmap]
rs2915477	0.85[CEU][hapmap]
rs2915479	0.84[CEU][hapmap]
rs2915480	0.85[CEU][hapmap]
rs2915481	0.85[CEU][hapmap]
rs2915482	0.85[CEU][hapmap]
rs2915483	0.85[CEU][hapmap]
rs2915484	0.85[CEU][hapmap]
rs2915485	0.85[CEU][hapmap]
rs2976984	0.85[CEU][hapmap]
rs2976985	0.85[CEU][hapmap]
rs2976986	0.85[CEU][hapmap]
rs2976988	0.85[CEU][hapmap]
rs2976989	0.85[CEU][hapmap]
rs2976990	0.85[CEU][hapmap]
rs2976991	0.85[CEU][hapmap]
rs2976992	0.89[CEU][hapmap]
rs2976993	0.85[CEU][hapmap]
rs2976994	0.85[CEU][hapmap]
rs2977006	0.88[YRI][hapmap]
rs2977013	0.83[ASW][hapmap]
rs2977016	0.83[ASW][hapmap]
rs3097703	0.85[CEU][hapmap]
rs3097704	0.85[CEU][hapmap]
rs3097705	0.85[CEU][hapmap]
rs3097706	0.85[CEU][hapmap]
rs3115784	0.85[CEU][hapmap]
rs4500070	1.00[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4873189	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4873530	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4873541	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6473594	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6473596	0.91[ASN][1000 genomes]
rs6984536	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6995702	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6996951	0.85[CEU][hapmap]
rs6998855	0.90[CEU][hapmap]
rs6999880	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7004460	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7016775	0.89[CEU][hapmap]
rs7017403	0.89[CEU][hapmap]
rs7017421	0.89[CEU][hapmap]
rs766788	0.85[CEU][hapmap]
rs766790	0.85[CEU][hapmap]
rs7813377	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7817771	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7827306	0.90[CEU][hapmap];0.90[MEX][hapmap]
rs7827446	0.90[CEU][hapmap];0.89[MEX][hapmap]
rs7828080	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7834299	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7840437	0.90[CEU][hapmap]
rs7842285	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7845311	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9298441	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9298443	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9298444	0.85[CEU][hapmap]
rs9657149	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs972025	0.85[CEU][hapmap]
rs972026	0.85[CEU][hapmap]
rs994127	0.83[ASW][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv2764079	chr8:51881783-52202880	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv465679	chr8:51883927-52189796	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv611350	chr8:51883927-52189796	Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1030378	chr8:51892949-52191830	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv948338	chr8:52060314-52368754	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv6189	chr8:52145834-52191132	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv982149	chr8:52185110-52191544	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3584889	chr8:52188402-52197148	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52184200-52197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:52188000-52191200	Enhancers	Fetal Brain Male	brain
3	chr8:52188200-52191200	Enhancers	Brain Germinal Matrix	brain
4	chr8:52188800-52191200	Enhancers	Fetal Brain Female	brain
5	chr8:52189200-52190800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr8:52189400-52190200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:52189400-52190400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:52189400-52190400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr8:52189600-52189800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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