Variant report

Variant	rs12594378
Chromosome Location	chr15:43051626-43051627
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12323990	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12324135	0.87[EUR][1000 genomes]
rs12591415	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12592374	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12592573	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594325	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12594600	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594696	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594699	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594724	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594725	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594765	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594837	0.93[ASN][1000 genomes]
rs12595722	0.88[ASN][1000 genomes]
rs16957043	0.87[EUR][1000 genomes]
rs16957055	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16957061	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16957063	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16957120	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1915242	0.87[EUR][1000 genomes]
rs1915243	0.87[EUR][1000 genomes]
rs28431056	0.95[ASN][1000 genomes]
rs28437884	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28542286	0.81[AFR][1000 genomes]
rs28661826	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28680600	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28699522	0.87[EUR][1000 genomes]
rs28736688	1.00[EUR][1000 genomes]
rs3742992	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3742995	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4334272	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56046122	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs56839966	0.87[EUR][1000 genomes]
rs58237318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58548142	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60723187	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61747153	0.93[ASN][1000 genomes]
rs7169231	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169238	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7178483	1.00[EUR][1000 genomes]
rs73408611	0.87[EUR][1000 genomes]
rs73408619	1.00[EUR][1000 genomes]
rs73410923	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410927	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410937	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410940	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73410959	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73410961	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410969	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410971	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410972	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410973	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73410981	0.87[EUR][1000 genomes]
rs8023743	1.00[EUR][1000 genomes]
rs8028365	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8028699	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033336	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8036733	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8043143	1.00[EUR][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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43029800-43071000	Weak transcription	Pancreas	Pancrea
2	chr15:43030000-43053200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:43030000-43053200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:43030000-43053800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:43030000-43066200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr15:43030000-43067200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:43030000-43093600	Weak transcription	Colonic Mucosa	Colon
8	chr15:43030200-43052800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:43038200-43055200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:43038400-43067400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:43044600-43056000	Weak transcription	Fetal Lung	lung
12	chr15:43044800-43052800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:43044800-43053000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:43044800-43053000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:43044800-43053200	Weak transcription	Osteobl	bone
16	chr15:43044800-43053600	Weak transcription	Aorta	Aorta
17	chr15:43044800-43054200	Weak transcription	Fetal Brain Male	brain
18	chr15:43044800-43066400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:43045000-43065600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:43045400-43051800	Weak transcription	Brain Angular Gyrus	brain
21	chr15:43045400-43052600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:43045400-43052800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:43045400-43053000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:43045400-43053200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:43045400-43062800	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:43045400-43068000	Weak transcription	Fetal Heart	heart
27	chr15:43045600-43053000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:43045600-43074400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:43045800-43064800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:43046000-43051800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr15:43046000-43052600	Weak transcription	Dnd41	blood
32	chr15:43046000-43052800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:43046000-43052800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:43046000-43054400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:43046000-43062600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:43046200-43052800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:43046200-43053000	Weak transcription	Primary B cells from cord blood	blood
38	chr15:43046200-43053000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr15:43050800-43051800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:43050800-43051800	Enhancers	Fetal Muscle Trunk	muscle
41	chr15:43050800-43051800	Enhancers	Fetal Muscle Leg	muscle
42	chr15:43050800-43052000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:43051000-43051800	Enhancers	Psoas Muscle	Psoas
44	chr15:43051000-43052000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr15:43051000-43052000	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr15:43051000-43052000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr15:43051200-43051800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr15:43051200-43051800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:43051200-43051800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:43051200-43051800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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