Variant report

Variant	rs13176737
Chromosome Location	chr5:50089520-50089521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10052372	0.96[EUR][1000 genomes]
rs11950506	0.89[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11952107	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11955651	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11955934	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11959326	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13155662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13156735	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13157079	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13159045	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13159239	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13159553	0.83[AMR][1000 genomes]
rs13161225	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13162738	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13163470	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13163802	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13166819	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13167408	0.83[AMR][1000 genomes]
rs13169153	1.00[EUR][1000 genomes]
rs13169200	0.83[AMR][1000 genomes]
rs13172426	0.83[AMR][1000 genomes]
rs13172836	0.83[AMR][1000 genomes]
rs13174498	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13180506	0.83[AMR][1000 genomes]
rs13181031	0.91[EUR][1000 genomes]
rs13181117	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13183686	0.83[AMR][1000 genomes]
rs13183910	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13186653	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13189183	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13190144	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16886309	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs34183555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34264957	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34414061	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34677483	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34758774	0.90[EUR][1000 genomes]
rs34827507	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34855203	0.87[EUR][1000 genomes]
rs35128589	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35210389	0.83[AMR][1000 genomes]
rs35292338	0.83[AMR][1000 genomes]
rs35347195	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35434227	0.83[AMR][1000 genomes]
rs35473824	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35596019	0.83[AMR][1000 genomes]
rs36187734	0.83[AMR][1000 genomes]
rs41270305	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6859621	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6880398	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6883701	0.88[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888271	0.87[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888315	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6892149	1.00[CEU][hapmap]
rs71615974	0.83[AMR][1000 genomes]
rs71615975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71615978	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71615981	0.92[EUR][1000 genomes]
rs71615983	1.00[EUR][1000 genomes]
rs71615984	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615986	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71615988	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71615990	0.96[EUR][1000 genomes]
rs71615991	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7717073	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7726225	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7733931	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[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	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	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
rs13176737	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50041800-50090000	Weak transcription	Small Intestine	intestine
2	chr5:50052800-50098800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:50057800-50090600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:50058000-50090600	Weak transcription	Aorta	Aorta
6	chr5:50058200-50092400	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:50064000-50126800	Weak transcription	Osteobl	bone
8	chr5:50068800-50090600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:50069600-50093400	Weak transcription	HMEC	breast
10	chr5:50069600-50095400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:50069600-50095400	Weak transcription	Fetal Lung	lung
12	chr5:50069600-50100000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:50070600-50098000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr5:50071400-50090600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:50071400-50093000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:50071400-50098200	Weak transcription	Fetal Intestine Small	intestine
17	chr5:50071400-50099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:50071400-50108000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr5:50071600-50138200	Weak transcription	Placenta	Placenta
20	chr5:50072200-50093400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr5:50073400-50092400	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:50073600-50095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:50075400-50092200	Weak transcription	Right Ventricle	heart
24	chr5:50076400-50090200	Weak transcription	Colonic Mucosa	Colon
25	chr5:50076600-50090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:50078000-50090600	Weak transcription	Esophagus	oesophagus
27	chr5:50078200-50140000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:50081000-50095000	Weak transcription	NHLF	lung
29	chr5:50081200-50092200	Strong transcription	Primary B cells from cord blood	blood
30	chr5:50081200-50098200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:50081400-50097400	Strong transcription	Primary T cells from cord blood	blood
32	chr5:50081400-50098200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:50081600-50091200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:50081600-50098600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr5:50081600-50098800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:50081800-50095200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:50082400-50095400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:50083000-50090600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:50083000-50090600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:50083200-50090600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:50083200-50092200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:50083200-50092400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr5:50083200-50095200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:50083200-50098800	Weak transcription	Brain Hippocampus Middle	brain
45	chr5:50083200-50116800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:50083400-50092600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:50083400-50092600	Weak transcription	Brain Angular Gyrus	brain
48	chr5:50083400-50092800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:50083400-50095400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:50083400-50097400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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