Variant report

Variant	rs13169153
Chromosome Location	chr5:50073078-50073079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10052372	0.96[EUR][1000 genomes]
rs11950506	1.00[EUR][1000 genomes]
rs11952107	0.87[EUR][1000 genomes]
rs11955651	0.92[EUR][1000 genomes]
rs11955934	0.96[EUR][1000 genomes]
rs11959326	0.85[EUR][1000 genomes]
rs13155662	1.00[EUR][1000 genomes]
rs13156735	0.92[EUR][1000 genomes]
rs13157079	0.92[EUR][1000 genomes]
rs13159045	0.94[EUR][1000 genomes]
rs13159239	0.87[EUR][1000 genomes]
rs13161225	0.94[EUR][1000 genomes]
rs13162738	0.92[EUR][1000 genomes]
rs13163470	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13163802	0.96[EUR][1000 genomes]
rs13166819	0.94[EUR][1000 genomes]
rs13174498	0.92[EUR][1000 genomes]
rs13176737	1.00[EUR][1000 genomes]
rs13181031	0.91[EUR][1000 genomes]
rs13181117	0.92[EUR][1000 genomes]
rs13183910	0.92[EUR][1000 genomes]
rs13186653	1.00[EUR][1000 genomes]
rs13189183	0.94[EUR][1000 genomes]
rs13190144	0.85[EUR][1000 genomes]
rs16886309	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34183555	0.85[EUR][1000 genomes]
rs34264957	0.85[EUR][1000 genomes]
rs34414061	0.90[EUR][1000 genomes]
rs34677483	0.92[EUR][1000 genomes]
rs34758774	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34827507	1.00[EUR][1000 genomes]
rs34855203	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35128589	0.87[EUR][1000 genomes]
rs35347195	1.00[EUR][1000 genomes]
rs35473824	0.92[EUR][1000 genomes]
rs41270305	0.94[EUR][1000 genomes]
rs6859621	0.87[EUR][1000 genomes]
rs6880398	0.92[EUR][1000 genomes]
rs6883701	1.00[EUR][1000 genomes]
rs6888271	1.00[EUR][1000 genomes]
rs6888315	1.00[EUR][1000 genomes]
rs71615978	0.87[EUR][1000 genomes]
rs71615981	0.92[EUR][1000 genomes]
rs71615983	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615984	1.00[EUR][1000 genomes]
rs71615986	1.00[EUR][1000 genomes]
rs71615988	0.94[EUR][1000 genomes]
rs71615990	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71615991	0.94[EUR][1000 genomes]
rs7717073	0.87[EUR][1000 genomes]
rs7726225	0.87[EUR][1000 genomes]
rs7733931	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598110	chr5:49988020-50089919	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv462163	chr5:49989701-50088317	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv598113	chr5:49989701-50088317	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv598114	chr5:49991561-50088317	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13169153	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50041800-50090000	Weak transcription	Small Intestine	intestine
2	chr5:50051200-50084600	Weak transcription	NHEK	skin
3	chr5:50052000-50078000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:50052800-50098800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:50057800-50084600	Weak transcription	Ovary	ovary
7	chr5:50057800-50090600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:50058000-50090600	Weak transcription	Aorta	Aorta
9	chr5:50058200-50075200	Weak transcription	Gastric	stomach
10	chr5:50058200-50084600	Weak transcription	Fetal Thymus	thymus
11	chr5:50058200-50092400	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:50060200-50084600	Weak transcription	Thymus	Thymus
13	chr5:50060400-50073400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:50060400-50081800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:50063200-50082800	Weak transcription	Fetal Heart	heart
16	chr5:50064000-50084400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:50064000-50126800	Weak transcription	Osteobl	bone
18	chr5:50066800-50084200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr5:50067800-50075400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:50068000-50084600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr5:50068200-50077800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:50068800-50090600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:50069000-50086400	Weak transcription	Stomach Mucosa	stomach
24	chr5:50069400-50073400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:50069400-50084200	Weak transcription	Liver	Liver
26	chr5:50069600-50073400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:50069600-50074800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:50069600-50074800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:50069600-50077200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:50069600-50077400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:50069600-50077400	Weak transcription	Adipose Nuclei	Adipose
32	chr5:50069600-50077400	Weak transcription	GM12878-XiMat	blood
33	chr5:50069600-50081600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:50069600-50084200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:50069600-50084400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:50069600-50084600	Weak transcription	Left Ventricle	heart
37	chr5:50069600-50084600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:50069600-50093400	Weak transcription	HMEC	breast
39	chr5:50069600-50095400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:50069600-50095400	Weak transcription	Fetal Lung	lung
41	chr5:50069600-50100000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr5:50070600-50098000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:50071000-50075000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:50071000-50077200	Weak transcription	Spleen	Spleen
45	chr5:50071000-50079400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr5:50071000-50084600	Weak transcription	Pancreas	Pancrea
47	chr5:50071200-50073200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:50071200-50073600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr5:50071200-50073800	Strong transcription	Dnd41	blood
50	chr5:50071400-50073200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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