Variant report

Variant	rs1826862
Chromosome Location	chr5:178390407-178390408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10464050	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1475949	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1475950	0.91[ASW][hapmap];0.89[CHB][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17078865	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17081834	0.85[EUR][1000 genomes]
rs2132673	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56740821	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56773504	0.85[EUR][1000 genomes]
rs56790802	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56954828	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59485557	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59515073	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60629856	0.81[ASN][1000 genomes]
rs61213092	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61314110	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6867653	0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs6871003	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73334703	0.81[EUR][1000 genomes]
rs73334721	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73334723	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73334729	0.87[ASN][1000 genomes]
rs73334737	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73336533	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73336535	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9637932	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600489	chr5:178368096-178430375	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1017941	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv537974	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3471133	chr5:178386746-178392344	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
5	esv3471134	chr5:178386746-178392344	ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
6	nsv823356	chr5:178389435-178391094	ZNF genes & repeats Weak transcription Strong transcription Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv883219	chr5:178390237-178454118	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178369400-178418200	ZNF genes & repeats	Fetal Brain Female	brain
2	chr5:178380000-178393600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr5:178381400-178394200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
4	chr5:178383400-178394400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:178384400-178395600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:178387000-178394200	ZNF genes & repeats	Fetal Muscle Leg	muscle
7	chr5:178387800-178394400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:178388600-178390600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:178388800-178393200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr5:178388800-178397000	ZNF genes & repeats	Brain Anterior Caudate	brain
11	chr5:178388800-178398600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr5:178389000-178393000	ZNF genes & repeats	Colon Smooth Muscle	Colon
13	chr5:178389000-178394200	ZNF genes & repeats	Fetal Lung	lung
14	chr5:178389000-178394400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:178389000-178398200	ZNF genes & repeats	Brain Hippocampus Middle	brain
16	chr5:178389200-178394000	ZNF genes & repeats	Ovary	ovary
17	chr5:178389200-178394400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
18	chr5:178389200-178394600	ZNF genes & repeats	Brain Substantia Nigra	brain
19	chr5:178389200-178398400	ZNF genes & repeats	Liver	Liver
20	chr5:178389400-178392600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:178389400-178400400	ZNF genes & repeats	Adipose Nuclei	Adipose
22	chr5:178389400-178405200	ZNF genes & repeats	Brain Germinal Matrix	brain
23	chr5:178389600-178390600	ZNF genes & repeats	Psoas Muscle	Psoas
24	chr5:178389600-178393000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
25	chr5:178389600-178394400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:178389600-178394400	ZNF genes & repeats	Fetal Brain Male	brain
27	chr5:178389600-178394400	ZNF genes & repeats	Left Ventricle	heart
28	chr5:178389600-178396200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
29	chr5:178389800-178390800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
30	chr5:178389800-178392200	ZNF genes & repeats	Aorta	Aorta
31	chr5:178389800-178392600	ZNF genes & repeats	Placenta Amnion	Placenta Amnion
32	chr5:178389800-178392800	ZNF genes & repeats	Pancreas	Pancrea
33	chr5:178389800-178393200	ZNF genes & repeats	Fetal Kidney	kidney
34	chr5:178389800-178394200	ZNF genes & repeats	Right Ventricle	heart
35	chr5:178389800-178398400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
36	chr5:178389800-178399600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:178389800-178400000	ZNF genes & repeats	Fetal Stomach	stomach
38	chr5:178390000-178390600	Weak transcription	Brain Angular Gyrus	brain
39	chr5:178390000-178391600	Weak transcription	Fetal Heart	heart
40	chr5:178390000-178392600	ZNF genes & repeats	Small Intestine	intestine
41	chr5:178390400-178390600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
42	chr5:178390400-178391400	ZNF genes & repeats	Fetal Intestine Large	intestine
43	chr5:178390400-178392200	ZNF genes & repeats	Lung	lung
44	chr5:178390400-178392600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
45	chr5:178390400-178392800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
46	chr5:178390400-178392800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin

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