Variant report

Variant	rs28661824
Chromosome Location	chr5:49735370-49735371
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	chr5:49731051..49732867-chr5:49733750..49736731,2	MCF-7	breast:

Extended variants
information (count: 126 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10041033	0.87[ASN][1000 genomes]
rs10042504	0.89[ASN][1000 genomes]
rs10055539	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10059354	0.82[ASN][1000 genomes]
rs10061339	0.88[ASN][1000 genomes]
rs10071725	0.85[ASN][1000 genomes]
rs10076490	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10079493	0.87[ASN][1000 genomes]
rs1016621	0.80[ASN][1000 genomes]
rs10214007	0.85[ASN][1000 genomes]
rs1039797	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10471362	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10940334	0.80[ASN][1000 genomes]
rs10940335	0.82[ASN][1000 genomes]
rs10940336	0.82[ASN][1000 genomes]
rs11948302	0.82[ASN][1000 genomes]
rs11948752	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11959569	0.87[ASN][1000 genomes]
rs12651909	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13153021	0.80[ASN][1000 genomes]
rs13155292	0.86[ASN][1000 genomes]
rs13157992	1.00[ASN][1000 genomes]
rs13159506	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13168063	0.82[ASN][1000 genomes]
rs13173678	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13174293	0.83[ASN][1000 genomes]
rs13180767	0.84[ASN][1000 genomes]
rs13180852	0.90[ASN][1000 genomes]
rs13184498	0.81[ASN][1000 genomes]
rs13185587	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13357429	0.92[ASN][1000 genomes]
rs1606226	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16879094	0.95[ASN][1000 genomes]
rs1811742	0.92[ASN][1000 genomes]
rs1812994	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1833900	0.82[ASN][1000 genomes]
rs1849200	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1962832	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1995795	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2036901	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2036902	0.90[ASN][1000 genomes]
rs2089605	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2137132	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2137134	0.86[ASN][1000 genomes]
rs2271236	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353436	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2668024	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28445612	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28500170	0.98[ASN][1000 genomes]
rs28528780	0.95[ASN][1000 genomes]
rs28676351	0.93[ASN][1000 genomes]
rs2883164	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs303219	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs303231	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs303235	0.88[ASN][1000 genomes]
rs303237	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34044048	0.91[ASN][1000 genomes]
rs34044167	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34741488	0.88[ASN][1000 genomes]
rs34749302	0.87[ASN][1000 genomes]
rs34774804	0.81[ASN][1000 genomes]
rs34945845	0.87[ASN][1000 genomes]
rs34950042	0.83[ASN][1000 genomes]
rs36138717	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3849669	0.87[ASN][1000 genomes]
rs3849670	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3860732	0.88[ASN][1000 genomes]
rs3950451	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4029989	0.89[ASN][1000 genomes]
rs4030569	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4030570	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4030571	0.88[ASN][1000 genomes]
rs4030572	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4030573	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4031137	0.87[ASN][1000 genomes]
rs4082836	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4145844	0.86[ASN][1000 genomes]
rs4277861	0.82[ASN][1000 genomes]
rs4340921	0.81[ASN][1000 genomes]
rs4398636	0.89[ASN][1000 genomes]
rs4495185	0.92[ASN][1000 genomes]
rs4549528	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4563580	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4571473	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4637546	0.84[ASN][1000 genomes]
rs57137858	0.88[ASN][1000 genomes]
rs57583601	0.99[ASN][1000 genomes]
rs58756661	0.95[ASN][1000 genomes]
rs59254474	0.93[ASN][1000 genomes]
rs62365887	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62365896	0.93[ASN][1000 genomes]
rs62365901	1.00[ASN][1000 genomes]
rs62365902	0.97[ASN][1000 genomes]
rs62386175	0.83[ASN][1000 genomes]
rs6450056	0.83[ASN][1000 genomes]
rs6450063	0.88[ASN][1000 genomes]
rs6450098	0.92[ASN][1000 genomes]
rs6450099	0.89[ASN][1000 genomes]
rs6450107	0.93[ASN][1000 genomes]
rs6450139	0.90[ASN][1000 genomes]
rs6450164	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6868677	0.83[ASN][1000 genomes]
rs6869871	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6874829	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7446360	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7706105	0.82[ASN][1000 genomes]
rs7712749	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7712849	0.91[ASN][1000 genomes]
rs7717982	0.89[ASN][1000 genomes]
rs7721808	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7732000	0.85[ASN][1000 genomes]
rs9292005	0.94[ASN][1000 genomes]
rs9716734	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv3418391	chr5:49734766-49740307	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv3443771	chr5:49734989-49740073	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28661824	EMB	cis	Thyroid	GTEx
rs28661824	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs28661824	PARP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 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	chr5:49724200-49735800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:49727200-49736000	Weak transcription	HSMM	muscle
5	chr5:49727600-49735800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:49727800-49736400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:49728000-49735800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:49728200-49736000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:49731400-49735400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:49731400-49735600	Weak transcription	Thymus	Thymus
11	chr5:49731600-49736000	Weak transcription	Small Intestine	intestine
12	chr5:49731800-49736000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:49735000-49735600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr5:49735000-49735600	Enhancers	Primary hematopoietic stem cells	blood
15	chr5:49735000-49735800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:49735000-49735800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:49735000-49735800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:49735000-49735800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr5:49735000-49735800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:49735000-49736000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr5:49735000-49736200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr5:49735000-49736200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr5:49735000-49736200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr5:49735000-49736200	Flanking Active TSS	Dnd41	blood
25	chr5:49735000-49736400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr5:49735000-49738000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:49735200-49735400	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr5:49735200-49735400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:49735200-49735400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr5:49735200-49735400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:49735200-49735400	Enhancers	Fetal Intestine Small	intestine
32	chr5:49735200-49735400	Enhancers	Fetal Thymus	thymus
33	chr5:49735200-49735600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr5:49735200-49735800	Enhancers	Primary B cells from peripheral blood	blood
35	chr5:49735200-49735800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:49735200-49735800	Enhancers	Fetal Intestine Large	intestine
37	chr5:49735200-49735800	Enhancers	NHEK	skin
38	chr5:49735200-49736000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr5:49735200-49736200	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr5:49735200-49736200	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr5:49735200-49736200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:49735200-49736400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:49735200-49736600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr5:49735200-49737400	Active TSS	HMEC	breast
45	chr5:49735200-49738200	Active TSS	Duodenum Mucosa	Duodenum

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