Variant report

Variant	rs6860503
Chromosome Location	chr5:49742174-49742175
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	chr5:49736414..49737923-chr5:49740071..49742726,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170571	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10042504	0.82[EUR][1000 genomes]
rs10043101	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10059354	0.87[EUR][1000 genomes]
rs10061339	0.95[EUR][1000 genomes]
rs10071725	0.80[EUR][1000 genomes]
rs10072182	0.88[ASN][1000 genomes]
rs10073530	0.88[ASN][1000 genomes]
rs1010676	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1016621	0.87[EUR][1000 genomes]
rs1039798	0.87[ASN][1000 genomes]
rs10940334	0.89[EUR][1000 genomes]
rs10940335	0.89[EUR][1000 genomes]
rs10940336	0.89[EUR][1000 genomes]
rs11948302	0.89[EUR][1000 genomes]
rs11959569	0.80[EUR][1000 genomes]
rs12109228	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12659303	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13153021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13157992	0.99[EUR][1000 genomes]
rs13180579	0.90[ASN][1000 genomes]
rs13180852	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13182357	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13184466	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13184498	0.88[EUR][1000 genomes]
rs13184661	0.89[EUR][1000 genomes]
rs13357429	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1606226	0.80[ASN][1000 genomes]
rs16879094	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1811742	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1812936	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1833900	0.87[EUR][1000 genomes]
rs1849200	0.80[ASN][1000 genomes]
rs1967289	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2036902	0.84[EUR][1000 genomes]
rs2353436	0.80[ASN][1000 genomes]
rs28500170	0.99[EUR][1000 genomes]
rs28528780	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28676351	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs303231	0.80[ASN][1000 genomes]
rs34044048	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34185098	0.86[ASN][1000 genomes]
rs34433187	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34741488	0.82[EUR][1000 genomes]
rs34774804	0.91[EUR][1000 genomes]
rs34945845	0.87[EUR][1000 genomes]
rs34950042	0.95[EUR][1000 genomes]
rs35858778	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35866059	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3849669	0.80[EUR][1000 genomes]
rs3860731	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3860732	0.80[EUR][1000 genomes]
rs3933097	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4029989	0.94[EUR][1000 genomes]
rs4030571	0.80[EUR][1000 genomes]
rs4031137	0.82[EUR][1000 genomes]
rs4145844	0.95[EUR][1000 genomes]
rs4277861	0.91[EUR][1000 genomes]
rs4398636	0.82[EUR][1000 genomes]
rs4495185	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57137858	0.80[EUR][1000 genomes]
rs57583601	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58756661	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59254474	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62365896	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62365901	0.98[EUR][1000 genomes]
rs62365902	0.92[EUR][1000 genomes]
rs62386175	0.82[EUR][1000 genomes]
rs6450063	0.82[EUR][1000 genomes]
rs6450098	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6450099	0.88[EUR][1000 genomes]
rs6450107	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6450139	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6868380	0.86[ASN][1000 genomes]
rs7442762	0.88[ASN][1000 genomes]
rs7706105	0.89[EUR][1000 genomes]
rs7712849	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7717982	0.84[EUR][1000 genomes]
rs7719081	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9292005	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9716734	0.88[EUR][1000 genomes]
rs9764793	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv980642	chr5:49739665-49754975	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6860503	EMB	cis	Skin Sun Exposed Lower leg	GTEx
rs6860503	EMB	cis	Whole Blood	GTEx
rs6860503	EMB	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49740400-49743400	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr5:49740600-49742600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr5:49740600-49742800	Enhancers	Primary B cells from peripheral blood	blood
4	chr5:49740600-49744800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr5:49740800-49742200	Enhancers	Primary hematopoietic stem cells	blood
6	chr5:49741400-49742200	Enhancers	Duodenum Mucosa	Duodenum
7	chr5:49741400-49742200	Flanking Active TSS	Dnd41	blood
8	chr5:49741600-49742200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr5:49741600-49742200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:49741600-49742200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr5:49741600-49742200	Enhancers	GM12878-XiMat	blood
12	chr5:49741600-49742400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr5:49741600-49742600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr5:49741600-49743600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:49741600-49744000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr5:49741600-49745400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:49741800-49742600	Enhancers	Primary B cells from cord blood	blood
18	chr5:49741800-49744000	Enhancers	Primary T cells from cord blood	blood
19	chr5:49741800-49744200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr5:49742000-49743800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:49742000-49743800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr5:49742000-49744400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr5:49742000-49745400	Weak transcription	Thymus	Thymus
24	chr5:49742000-49745600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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