Variant report

Variant	rs28454399
Chromosome Location	chr10:43081813-43081814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10128322	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11239664	0.83[EUR][1000 genomes]
rs11239695	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239707	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11239708	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11239709	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12219669	0.83[EUR][1000 genomes]
rs12240565	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12242735	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12245618	0.81[ASN][1000 genomes]
rs12247715	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12255518	0.88[AFR][1000 genomes]
rs12256744	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12256867	0.88[ASN][1000 genomes]
rs12260943	0.89[AFR][1000 genomes]
rs12260958	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12261023	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12261168	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12262549	0.94[ASN][1000 genomes]
rs12262782	0.89[AFR][1000 genomes]
rs12265792	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266387	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12268051	0.90[AFR][1000 genomes]
rs12268549	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12269593	0.86[AFR][1000 genomes]
rs1413393	0.94[ASN][1000 genomes]
rs17157476	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157513	0.94[ASN][1000 genomes]
rs17157528	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17158029	0.83[ASN][1000 genomes]
rs2297693	0.83[ASN][1000 genomes]
rs28404481	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3740326	0.83[EUR][1000 genomes]
rs41301639	0.85[ASN][1000 genomes]
rs55904273	0.83[AFR][1000 genomes]
rs55914715	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56355729	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57084246	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58635980	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs58877883	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs60433789	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7069467	1.00[ASN][1000 genomes]
rs7071990	1.00[ASN][1000 genomes]
rs7078390	1.00[ASN][1000 genomes]
rs7079577	1.00[ASN][1000 genomes]
rs7082367	1.00[ASN][1000 genomes]
rs7097766	0.94[ASN][1000 genomes]
rs7100293	0.81[ASN][1000 genomes]
rs73266634	0.88[ASN][1000 genomes]
rs74137906	0.89[AFR][1000 genomes]
rs74137907	0.89[AFR][1000 genomes]
rs74137908	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74137910	0.89[AFR][1000 genomes]
rs74137911	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs74137912	0.96[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs74137913	0.96[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs74137915	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74137917	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74137918	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74137928	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs74137929	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7900972	0.94[ASN][1000 genomes]
rs7903632	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7904627	1.00[ASN][1000 genomes]
rs7906532	0.81[ASN][1000 genomes]
rs7910969	1.00[ASN][1000 genomes]
rs7912057	1.00[ASN][1000 genomes]
rs7919880	0.94[ASN][1000 genomes]
rs7921658	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817455	chr10:42607635-43151812	Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv550670	chr10:42725663-43089965	Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv895064	chr10:42783481-43243325	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
10	nsv469725	chr10:42965130-43178323	Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv482513	chr10:42965130-43178323	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
14	nsv975073	chr10:43079185-43083666	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43076000-43088400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr10:43076400-43083000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr10:43076600-43083400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:43076800-43082400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:43076800-43083000	Weak transcription	Thymus	Thymus
6	chr10:43076800-43087000	Weak transcription	Fetal Heart	heart
7	chr10:43077000-43083000	Weak transcription	Left Ventricle	heart
8	chr10:43077000-43083000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:43077600-43088000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:43077800-43083000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:43077800-43109600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:43079200-43082400	Weak transcription	Placenta	Placenta
13	chr10:43079600-43082000	Weak transcription	Primary T cells from cord blood	blood
14	chr10:43079600-43083000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:43079600-43083000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:43079800-43082000	Weak transcription	Ovary	ovary
17	chr10:43079800-43082800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:43080000-43082200	Weak transcription	Brain Germinal Matrix	brain
19	chr10:43080000-43082400	Weak transcription	Gastric	stomach
20	chr10:43080000-43082600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr10:43080000-43082600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr10:43080000-43083000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr10:43080000-43083200	Weak transcription	NHEK	skin
24	chr10:43080000-43083400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:43080200-43083000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:43080200-43083000	Weak transcription	Fetal Thymus	thymus
27	chr10:43080400-43082400	Weak transcription	Fetal Stomach	stomach
28	chr10:43080600-43082800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr10:43080600-43086600	Weak transcription	Stomach Mucosa	stomach
30	chr10:43080800-43082200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:43080800-43082400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr10:43080800-43082400	Weak transcription	Pancreas	Pancrea
33	chr10:43080800-43088000	Weak transcription	Right Ventricle	heart
34	chr10:43081000-43083000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr10:43081000-43083000	Strong transcription	Primary hematopoietic stem cells	blood
36	chr10:43081000-43083000	Weak transcription	Colonic Mucosa	Colon
37	chr10:43081000-43083000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr10:43081000-43083200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:43081000-43087200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr10:43081000-43087800	Weak transcription	Brain Hippocampus Middle	brain
41	chr10:43081000-43087800	Weak transcription	Psoas Muscle	Psoas
42	chr10:43081200-43082200	Weak transcription	Fetal Lung	lung
43	chr10:43081200-43082800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:43081200-43083000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr10:43081200-43083000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr10:43081200-43083400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr10:43081400-43082000	Weak transcription	Fetal Brain Female	brain
48	chr10:43081400-43083000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr10:43081400-43085400	Strong transcription	Primary B cells from cord blood	blood
50	chr10:43081400-43087800	Weak transcription	Brain Anterior Caudate	brain

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