Variant report

Variant	rs1967289
Chromosome Location	chr5:49702600-49702601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10043101	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10072182	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10073530	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1010676	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1039798	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12109228	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12659303	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13153021	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13180579	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13182357	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13184466	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13357429	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16879094	0.82[ASN][1000 genomes]
rs1811742	0.81[ASN][1000 genomes]
rs1812936	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2036902	0.83[ASN][1000 genomes]
rs28528780	0.82[ASN][1000 genomes]
rs303219	0.80[ASN][1000 genomes]
rs34185098	0.87[ASN][1000 genomes]
rs34433187	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35858778	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35866059	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3860731	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3933097	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4495185	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58756661	0.82[ASN][1000 genomes]
rs62365887	0.80[ASN][1000 genomes]
rs62365896	0.83[ASN][1000 genomes]
rs6450098	0.82[ASN][1000 genomes]
rs6450107	0.82[ASN][1000 genomes]
rs6860503	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6868380	0.87[ASN][1000 genomes]
rs7442762	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7712849	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7717982	0.82[ASN][1000 genomes]
rs7719081	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9292005	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	nsv1019539	chr5:49455624-49702736	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1023402	chr5:49455624-49708458	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1967289	EMB	cis	Whole Blood	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49682000-49719000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:49688800-49707200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:49688800-49710000	Weak transcription	Fetal Thymus	thymus
4	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:49690400-49708600	Strong transcription	Dnd41	blood
6	chr5:49690600-49706800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:49690800-49702600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:49691000-49702600	Weak transcription	HMEC	breast
9	chr5:49692800-49708000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:49693000-49707600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:49693400-49707000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:49694200-49707000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:49694400-49702600	Weak transcription	Fetal Intestine Large	intestine
14	chr5:49694600-49706400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:49695200-49705800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr5:49695600-49708400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:49697400-49702600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:49697400-49723400	Weak transcription	HSMM	muscle
20	chr5:49697600-49709800	Weak transcription	Primary T cells from cord blood	blood
21	chr5:49697600-49719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:49698200-49702800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:49698200-49711600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:49699400-49702800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:49699800-49702800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:49700800-49702600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:49701000-49702600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr5:49701000-49702600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr5:49701000-49702800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:49701000-49703000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:49701000-49705000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:49701000-49711400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:49701600-49702600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:49702000-49703800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr5:49702000-49705800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr5:49702200-49702600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr5:49702400-49703200	Enhancers	Primary B cells from cord blood	blood
39	chr5:49702400-49703200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr5:49702400-49703600	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr5:49702400-49703600	Enhancers	NHEK	skin
42	chr5:49702600-49703000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr5:49702600-49703000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr5:49702600-49703200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:49702600-49703200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr5:49702600-49703200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr5:49702600-49703200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr5:49702600-49703200	Enhancers	Fetal Intestine Large	intestine
49	chr5:49702600-49703200	Enhancers	Hela-S3	cervix
50	chr5:49702600-49703200	Enhancers	HMEC	breast

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