Variant report

Variant	rs28528780
Chromosome Location	chr5:49737127-49737128
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:89745796..89746719-chr5:49736950..49737765,2	NB4	blood:

Variant related genes	Relation type
ENSG00000139318	Chromatin interaction

Extended variants
information (count: 150 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10041033	0.90[ASN][1000 genomes]
rs10042504	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10043101	0.81[EUR][1000 genomes]
rs10055539	0.88[ASN][1000 genomes]
rs10059354	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10061339	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10071725	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10076490	0.94[ASN][1000 genomes]
rs10079493	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1010676	0.87[EUR][1000 genomes]
rs1016621	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10214007	0.80[ASN][1000 genomes]
rs1039797	0.84[ASN][1000 genomes]
rs10471362	0.87[ASN][1000 genomes]
rs10940334	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10940335	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10940336	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11948302	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11948752	0.82[ASN][1000 genomes]
rs11959569	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12109228	0.81[EUR][1000 genomes]
rs12651909	0.92[ASN][1000 genomes]
rs12659303	0.80[EUR][1000 genomes]
rs13153021	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13155292	0.84[ASN][1000 genomes]
rs13157992	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13159506	0.91[ASN][1000 genomes]
rs13173678	0.93[ASN][1000 genomes]
rs13174293	0.87[ASN][1000 genomes]
rs13180767	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13180852	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13182357	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13184466	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13184498	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13184661	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13185587	0.87[ASN][1000 genomes]
rs13357429	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1344339	0.81[ASN][1000 genomes]
rs1606226	0.94[ASN][1000 genomes]
rs16879094	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1811742	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1812936	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1812994	0.87[ASN][1000 genomes]
rs1833900	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1849200	0.94[ASN][1000 genomes]
rs1962832	0.82[ASN][1000 genomes]
rs1967289	0.82[ASN][1000 genomes]
rs1995795	0.84[ASN][1000 genomes]
rs2036901	0.90[ASN][1000 genomes]
rs2036902	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2089605	0.89[ASN][1000 genomes]
rs2137132	0.84[ASN][1000 genomes]
rs2137134	0.84[ASN][1000 genomes]
rs2271236	0.90[ASN][1000 genomes]
rs2353436	0.94[ASN][1000 genomes]
rs2668024	0.92[ASN][1000 genomes]
rs28445612	0.95[ASN][1000 genomes]
rs28500170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28661824	0.95[ASN][1000 genomes]
rs28676351	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2883164	0.90[ASN][1000 genomes]
rs303219	0.91[ASN][1000 genomes]
rs303231	0.94[ASN][1000 genomes]
rs303235	0.86[ASN][1000 genomes]
rs303237	0.87[ASN][1000 genomes]
rs34044048	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34044167	0.91[ASN][1000 genomes]
rs34433187	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34601168	0.81[ASN][1000 genomes]
rs34741488	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34749302	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34774804	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34945845	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34950042	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35740733	0.83[ASN][1000 genomes]
rs35858778	0.89[EUR][1000 genomes]
rs35866059	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36138717	0.92[ASN][1000 genomes]
rs3849669	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3849670	0.87[ASN][1000 genomes]
rs3860731	0.80[EUR][1000 genomes]
rs3860732	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3933097	0.80[ASN][1000 genomes]
rs3950451	0.91[ASN][1000 genomes]
rs4029989	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4030569	0.92[ASN][1000 genomes]
rs4030570	0.92[ASN][1000 genomes]
rs4030571	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4030572	0.88[ASN][1000 genomes]
rs4030573	0.92[ASN][1000 genomes]
rs4031137	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4082836	0.95[ASN][1000 genomes]
rs4145844	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4277861	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4337857	0.83[ASN][1000 genomes]
rs4398636	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4495185	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4549528	0.92[ASN][1000 genomes]
rs4563580	0.82[ASN][1000 genomes]
rs4571473	0.86[ASN][1000 genomes]
rs4637546	0.88[ASN][1000 genomes]
rs57137858	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57583601	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58756661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59254474	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62365887	0.91[ASN][1000 genomes]
rs62365896	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62365901	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62365902	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62386175	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6450056	0.88[ASN][1000 genomes]
rs6450063	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450098	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6450099	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6450107	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6450139	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6450164	0.82[ASN][1000 genomes]
rs6860503	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6863840	0.81[ASN][1000 genomes]
rs6868677	0.87[ASN][1000 genomes]
rs6869871	0.89[ASN][1000 genomes]
rs6871761	0.81[ASN][1000 genomes]
rs6874829	0.84[ASN][1000 genomes]
rs6877713	0.81[ASN][1000 genomes]
rs6897412	0.83[ASN][1000 genomes]
rs7446360	0.89[ASN][1000 genomes]
rs7706105	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7712749	0.90[ASN][1000 genomes]
rs7712849	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7717982	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7719081	0.90[EUR][1000 genomes]
rs7721808	0.87[ASN][1000 genomes]
rs7730857	0.83[ASN][1000 genomes]
rs7732000	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9292005	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9716734	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9764793	0.80[EUR][1000 genomes];0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28528780	EMB	cis	Thyroid	GTEx
rs28528780	EMB	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49735000-49738000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:49735200-49737400	Active TSS	HMEC	breast
3	chr5:49735200-49738200	Active TSS	Duodenum Mucosa	Duodenum
4	chr5:49735400-49737600	Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr5:49735400-49737800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr5:49735600-49737200	Active TSS	Primary T cells fromperipheralblood	blood
7	chr5:49735600-49737800	Active TSS	Thymus	Thymus
8	chr5:49735800-49737400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:49735800-49737400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr5:49735800-49737600	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr5:49735800-49737600	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr5:49735800-49737600	Active TSS	Rectal Smooth Muscle	rectum
13	chr5:49735800-49737800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:49735800-49737800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:49735800-49738000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr5:49735800-49738000	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr5:49736000-49737200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr5:49736000-49737200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
19	chr5:49736000-49737200	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr5:49736000-49737400	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr5:49736000-49737400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr5:49736000-49737400	Active TSS	Small Intestine	intestine
23	chr5:49736000-49737400	Active TSS	Stomach Mucosa	stomach
24	chr5:49736000-49737400	Active TSS	HSMM	muscle
25	chr5:49736000-49737600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr5:49736000-49737600	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr5:49736000-49737600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:49736000-49737600	Active TSS	Colonic Mucosa	Colon
29	chr5:49736000-49737600	Active TSS	Esophagus	oesophagus
30	chr5:49736000-49737800	Active TSS	H9 Cell Line	embryonic stem cell
31	chr5:49736000-49737800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:49736000-49737800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:49736000-49737800	Active TSS	Fetal Intestine Small	intestine
34	chr5:49736000-49737800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr5:49736000-49738400	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr5:49736200-49737200	Active TSS	Primary monocytes fromperipheralblood	blood
37	chr5:49736200-49737200	Active TSS	Primary B cells from peripheral blood	blood
38	chr5:49736200-49737200	Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr5:49736200-49737200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:49736200-49737200	Active TSS	Fetal Intestine Large	intestine
41	chr5:49736200-49737200	Active TSS	Fetal Thymus	thymus
42	chr5:49736200-49737400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:49736200-49737400	Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr5:49736200-49737400	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr5:49736200-49737400	Active TSS	Liver	Liver
46	chr5:49736200-49737600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr5:49736200-49737600	Active TSS	Primary T cells from cord blood	blood
48	chr5:49736200-49737600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr5:49736200-49737600	Active TSS	Dnd41	blood
50	chr5:49736200-49737800	Active TSS	iPS-15b Cell Line	embryonic stem cell

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