Variant report

Variant	rs13189140
Chromosome Location	chr5:49721346-49721347
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13154421	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13158256	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs13160401	1.00[AFR][1000 genomes]
rs13165145	1.00[AFR][1000 genomes]
rs13169411	0.96[EUR][1000 genomes]
rs13174803	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13185634	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17192300	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17192503	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17800685	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1962207	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34434894	1.00[AFR][1000 genomes]
rs34836131	1.00[AFR][1000 genomes]
rs34982640	0.84[AMR][1000 genomes]
rs35005767	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35290633	1.00[AFR][1000 genomes]
rs35647517	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35703604	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35831659	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36108557	0.81[EUR][1000 genomes]
rs3860733	0.93[AMR][1000 genomes]
rs61133464	0.96[EUR][1000 genomes]
rs6893317	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71631457	1.00[AFR][1000 genomes]
rs71631459	1.00[AFR][1000 genomes]
rs71631461	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71631463	0.82[AMR][1000 genomes]
rs71631464	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71631467	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71631475	1.00[AFR][1000 genomes]
rs7709512	0.82[AMR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13189140	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:49697400-49723400	Weak transcription	HSMM	muscle
4	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:49703200-49724600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:49703200-49727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:49713000-49722000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr5:49713000-49722600	Weak transcription	Fetal Thymus	thymus
9	chr5:49713000-49725800	Weak transcription	Small Intestine	intestine
10	chr5:49715000-49722600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:49715000-49723400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:49715000-49723800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:49716600-49722000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:49717000-49723600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:49717200-49722000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:49717800-49723800	Strong transcription	Dnd41	blood
17	chr5:49718200-49721800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:49718400-49727400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:49718600-49721400	Weak transcription	Primary B cells from cord blood	blood
20	chr5:49719000-49722800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:49719200-49721400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:49719200-49726800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:49719400-49723600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr5:49719600-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:49719600-49723800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:49719800-49724000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:49720000-49723600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:49720200-49724200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr5:49720400-49722800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:49720400-49723400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:49720400-49723400	Weak transcription	HMEC	breast
32	chr5:49720400-49723800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr5:49720400-49723800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:49720400-49736400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:49720400-49736400	Weak transcription	Spleen	Spleen
36	chr5:49720600-49721600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr5:49720600-49726000	Weak transcription	NHEK	skin
38	chr5:49720600-49726400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:49720600-49726800	Weak transcription	HSMMtube	muscle
40	chr5:49720800-49723600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:49721200-49723800	Strong transcription	Primary T cells from cord blood	blood

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