Variant report

Variant	rs55928960
Chromosome Location	chr5:80151973-80151974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1008119	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10942930	0.93[ASN][1000 genomes]
rs10942931	0.84[ASN][1000 genomes]
rs12522063	0.84[ASN][1000 genomes]
rs1592878	0.88[ASN][1000 genomes]
rs16878204	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979005	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3797897	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4703819	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4704685	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4704686	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704687	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56382955	0.85[ASN][1000 genomes]
rs57067128	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58508689	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151892	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151901	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151906	0.88[ASN][1000 genomes]
rs6151909	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864713	0.83[ASN][1000 genomes]
rs6869680	0.81[ASN][1000 genomes]
rs6885935	0.84[ASN][1000 genomes]
rs72765588	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72765590	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72765599	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72767343	0.82[ASN][1000 genomes]
rs73137557	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
2	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
4	chr5:80125200-80161600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:80137600-80152600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:80141200-80161000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:80141200-80178800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:80142000-80152600	Weak transcription	Brain Angular Gyrus	brain
9	chr5:80143000-80175400	Weak transcription	HMEC	breast
10	chr5:80143800-80156600	Weak transcription	Osteobl	bone
11	chr5:80145400-80152600	Weak transcription	Fetal Kidney	kidney
12	chr5:80145600-80152600	Weak transcription	Fetal Lung	lung
13	chr5:80145600-80153800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr5:80145600-80157000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:80145600-80172800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:80145600-80175600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr5:80145600-80181000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:80145800-80167400	Weak transcription	Placenta	Placenta
19	chr5:80145800-80173400	Weak transcription	Colonic Mucosa	Colon
20	chr5:80146000-80173400	Weak transcription	Esophagus	oesophagus
21	chr5:80146400-80152400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:80146400-80162600	Weak transcription	Fetal Stomach	stomach
23	chr5:80146400-80162800	Weak transcription	Gastric	stomach
24	chr5:80146400-80167200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:80146400-80167200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:80146400-80170600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:80146400-80173400	Weak transcription	Brain Substantia Nigra	brain
28	chr5:80146600-80152600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:80146600-80152600	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:80146600-80162000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:80146800-80152600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:80146800-80152600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:80146800-80161600	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:80146800-80161800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:80148400-80167400	Weak transcription	HSMM	muscle
36	chr5:80148600-80175600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr5:80148800-80156800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr5:80148800-80173200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:80149000-80161800	Weak transcription	HepG2	liver
40	chr5:80149200-80153800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:80149200-80157000	Weak transcription	HSMMtube	muscle
42	chr5:80149200-80166000	Weak transcription	K562	blood
43	chr5:80149200-80167200	Weak transcription	Hela-S3	cervix
44	chr5:80149200-80176200	Weak transcription	Colon Smooth Muscle	Colon
45	chr5:80149800-80180000	Weak transcription	Psoas Muscle	Psoas
46	chr5:80150000-80152400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:80150000-80153000	Strong transcription	Liver	Liver
48	chr5:80150000-80153000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr5:80150200-80153000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:80150200-80153200	Weak transcription	NHLF	lung

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