Variant report

Variant	rs58548142
Chromosome Location	chr15:43053522-43053523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11632809	0.87[AFR][1000 genomes]
rs12323990	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12324135	0.87[EUR][1000 genomes]
rs12591415	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12592374	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12592573	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594325	0.98[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12594378	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594600	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594696	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594699	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594724	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594725	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594765	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594837	0.90[ASN][1000 genomes]
rs12595722	0.85[ASN][1000 genomes]
rs16957043	0.87[EUR][1000 genomes]
rs16957055	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16957061	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16957063	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16957120	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1915242	0.87[EUR][1000 genomes]
rs1915243	0.87[EUR][1000 genomes]
rs28431056	0.93[ASN][1000 genomes]
rs28437884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28542286	0.90[AFR][1000 genomes]
rs28661826	0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28680600	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28699522	0.87[EUR][1000 genomes]
rs28736688	1.00[EUR][1000 genomes]
rs34302400	0.87[AFR][1000 genomes]
rs3742992	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3742995	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4334272	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56046122	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs56839966	0.87[EUR][1000 genomes]
rs58237318	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60723187	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61747153	0.90[ASN][1000 genomes]
rs6493065	0.81[AFR][1000 genomes]
rs7169231	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169238	0.89[AFR][1000 genomes]
rs7178483	1.00[EUR][1000 genomes]
rs7181238	0.88[AFR][1000 genomes]
rs73408611	0.87[EUR][1000 genomes]
rs73408619	1.00[EUR][1000 genomes]
rs73410923	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73410927	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410931	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410937	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410940	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs73410959	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs73410961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410969	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410972	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410973	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410981	0.87[EUR][1000 genomes]
rs8023743	1.00[EUR][1000 genomes]
rs8028365	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8028699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8033336	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8036733	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8042980	0.87[AFR][1000 genomes]
rs8043143	1.00[EUR][1000 genomes]
rs9920562	0.87[AFR][1000 genomes]
rs9920935	0.80[AFR][1000 genomes]
rs9944270	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43029800-43071000	Weak transcription	Pancreas	Pancrea
2	chr15:43030000-43053800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:43030000-43066200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:43030000-43067200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:43030000-43093600	Weak transcription	Colonic Mucosa	Colon
6	chr15:43038200-43055200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:43038400-43067400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:43044600-43056000	Weak transcription	Fetal Lung	lung
9	chr15:43044800-43053600	Weak transcription	Aorta	Aorta
10	chr15:43044800-43054200	Weak transcription	Fetal Brain Male	brain
11	chr15:43044800-43066400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:43045000-43065600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:43045400-43062800	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:43045400-43068000	Weak transcription	Fetal Heart	heart
15	chr15:43045600-43074400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:43045800-43064800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:43046000-43054400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:43046000-43062600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:43051800-43064000	Weak transcription	Left Ventricle	heart
20	chr15:43051800-43064400	Weak transcription	Fetal Stomach	stomach
21	chr15:43051800-43065200	Weak transcription	Placenta	Placenta
22	chr15:43051800-43066200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:43051800-43069400	Weak transcription	Gastric	stomach
24	chr15:43051800-43070600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:43051800-43074600	Weak transcription	Right Ventricle	heart
26	chr15:43051800-43075000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:43051800-43083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:43052000-43055800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:43052000-43063800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:43052000-43065800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:43052000-43065800	Weak transcription	Thymus	Thymus
32	chr15:43052000-43066000	Weak transcription	Spleen	Spleen
33	chr15:43052000-43066600	Weak transcription	Ovary	ovary
34	chr15:43052000-43074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:43052600-43054000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
36	chr15:43052800-43053600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
37	chr15:43052800-43053800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
38	chr15:43052800-43053800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
39	chr15:43052800-43053800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:43052800-43054000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:43052800-43054000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
42	chr15:43052800-43057600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:43053000-43054000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr15:43053000-43054400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:43053000-43054600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
46	chr15:43053000-43054800	ZNF genes & repeats	Primary B cells from cord blood	blood
47	chr15:43053200-43053600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
48	chr15:43053200-43054000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:43053200-43055200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood

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