Variant report

Variant	rs62365901
Chromosome Location	chr5:49730331-49730332
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49730001..49733814-chr5:49735437..49737964,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170571	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10041033	0.87[ASN][1000 genomes]
rs10042504	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10043101	0.81[EUR][1000 genomes]
rs10055539	0.90[ASN][1000 genomes]
rs10059354	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10061339	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10071725	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10076490	0.89[ASN][1000 genomes]
rs10079493	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1010676	0.86[EUR][1000 genomes]
rs1016621	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10214007	0.85[ASN][1000 genomes]
rs1039797	0.86[ASN][1000 genomes]
rs10471362	0.88[ASN][1000 genomes]
rs10940334	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10940335	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10940336	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11948302	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11948752	0.86[ASN][1000 genomes]
rs11959569	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12109228	0.81[EUR][1000 genomes]
rs12651909	0.88[ASN][1000 genomes]
rs13153021	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13155292	0.86[ASN][1000 genomes]
rs13157992	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159506	0.94[ASN][1000 genomes]
rs13168063	0.82[ASN][1000 genomes]
rs13173678	0.96[ASN][1000 genomes]
rs13174293	0.83[ASN][1000 genomes]
rs13180767	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13180852	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13182357	0.86[EUR][1000 genomes]
rs13184466	0.89[EUR][1000 genomes]
rs13184498	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13184661	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13185587	0.88[ASN][1000 genomes]
rs13357429	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1606226	0.99[ASN][1000 genomes]
rs16879094	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1811742	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1812936	0.91[EUR][1000 genomes]
rs1812994	0.88[ASN][1000 genomes]
rs1833900	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1849200	0.99[ASN][1000 genomes]
rs1962832	0.86[ASN][1000 genomes]
rs1995795	0.86[ASN][1000 genomes]
rs2036901	0.93[ASN][1000 genomes]
rs2036902	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2089605	0.91[ASN][1000 genomes]
rs2137132	0.86[ASN][1000 genomes]
rs2137134	0.86[ASN][1000 genomes]
rs2271236	0.93[ASN][1000 genomes]
rs2353436	0.99[ASN][1000 genomes]
rs2668024	0.95[ASN][1000 genomes]
rs28445612	1.00[ASN][1000 genomes]
rs28500170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28528780	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28661824	1.00[ASN][1000 genomes]
rs28676351	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2883164	0.92[ASN][1000 genomes]
rs303219	0.94[ASN][1000 genomes]
rs303231	0.99[ASN][1000 genomes]
rs303235	0.88[ASN][1000 genomes]
rs303237	0.88[ASN][1000 genomes]
rs34044048	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34044167	0.94[ASN][1000 genomes]
rs34433187	0.96[EUR][1000 genomes]
rs34741488	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34749302	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34774804	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34945845	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34950042	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35858778	0.89[EUR][1000 genomes]
rs35866059	0.86[EUR][1000 genomes]
rs36138717	0.97[ASN][1000 genomes]
rs3849669	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3849670	0.88[ASN][1000 genomes]
rs3860732	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3950451	0.87[ASN][1000 genomes]
rs4029989	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4030569	0.88[ASN][1000 genomes]
rs4030570	0.88[ASN][1000 genomes]
rs4030571	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4030572	0.90[ASN][1000 genomes]
rs4030573	0.87[ASN][1000 genomes]
rs4031137	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4082836	0.99[ASN][1000 genomes]
rs4145844	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4277861	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4340921	0.81[ASN][1000 genomes]
rs4398636	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4495185	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4549528	0.88[ASN][1000 genomes]
rs4563580	0.86[ASN][1000 genomes]
rs4571473	0.88[ASN][1000 genomes]
rs4637546	0.84[ASN][1000 genomes]
rs57137858	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57583601	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58756661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59254474	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62365887	0.94[ASN][1000 genomes]
rs62365896	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62365902	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62386175	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6450056	0.83[ASN][1000 genomes]
rs6450063	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6450098	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450099	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6450107	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6450139	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6450164	0.86[ASN][1000 genomes]
rs6860503	0.98[EUR][1000 genomes]
rs6868677	0.83[ASN][1000 genomes]
rs6869871	0.91[ASN][1000 genomes]
rs6874829	0.86[ASN][1000 genomes]
rs7446360	0.91[ASN][1000 genomes]
rs7706105	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7712749	0.93[ASN][1000 genomes]
rs7712849	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7717982	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7719081	0.91[EUR][1000 genomes]
rs7721808	0.88[ASN][1000 genomes]
rs7732000	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9292005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9716734	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9764793	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62365901	EMB	cis	Thyroid	GTEx
rs62365901	EMB	cis	Whole Blood	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49720400-49736400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:49720400-49736400	Weak transcription	Spleen	Spleen
3	chr5:49723600-49735200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr5:49724000-49733400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr5:49724200-49731000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:49724200-49735800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:49724400-49730400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:49724600-49730400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr5:49724600-49732400	Enhancers	Primary T cells from cord blood	blood
10	chr5:49724800-49732800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:49726000-49731400	Weak transcription	Small Intestine	intestine
12	chr5:49726400-49735000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr5:49726800-49731000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:49727200-49732400	Enhancers	Dnd41	blood
15	chr5:49727200-49734400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:49727200-49736000	Weak transcription	HSMM	muscle
17	chr5:49727400-49731400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:49727400-49735000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr5:49727400-49735200	Weak transcription	Fetal Thymus	thymus
20	chr5:49727600-49730600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr5:49727600-49735000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:49727600-49735800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:49727800-49736400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr5:49728000-49735800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:49728200-49736000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr5:49728600-49730400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr5:49728600-49735200	Weak transcription	NHEK	skin
28	chr5:49728800-49733600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr5:49729200-49735000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:49729400-49733400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:49729600-49730600	Genic enhancers	Primary B cells from cord blood	blood
32	chr5:49729600-49730600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:49729600-49730800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:49729600-49731000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr5:49729600-49731400	Enhancers	Primary B cells from peripheral blood	blood
36	chr5:49729600-49731400	Enhancers	Duodenum Mucosa	Duodenum
37	chr5:49729800-49732400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:49730000-49735000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr5:49730200-49730400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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