Variant report

Variant	rs28669038
Chromosome Location	chr19:40654076-40654077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10414087	1.00[ASN][1000 genomes]
rs10418532	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421829	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424773	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881677	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11882464	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882490	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163212	1.00[ASN][1000 genomes]
rs17756648	0.83[ASN][1000 genomes]
rs234329	1.00[ASN][1000 genomes]
rs234338	1.00[ASN][1000 genomes]
rs2531363	1.00[ASN][1000 genomes]
rs337796	1.00[ASN][1000 genomes]
rs383975	1.00[ASN][1000 genomes]
rs399405	1.00[ASN][1000 genomes]
rs420413	1.00[ASN][1000 genomes]
rs445379	1.00[ASN][1000 genomes]
rs517342	1.00[ASN][1000 genomes]
rs520877	1.00[ASN][1000 genomes]
rs526467	1.00[ASN][1000 genomes]
rs532235	1.00[ASN][1000 genomes]
rs563703	1.00[ASN][1000 genomes]
rs589279	1.00[ASN][1000 genomes]
rs589404	1.00[ASN][1000 genomes]
rs62106576	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106577	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106578	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106580	0.83[ASN][1000 genomes]
rs62106581	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62106584	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106585	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62106586	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106587	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106588	1.00[ASN][1000 genomes]
rs62106589	1.00[ASN][1000 genomes]
rs62106590	1.00[ASN][1000 genomes]
rs62106591	1.00[ASN][1000 genomes]
rs62106625	1.00[ASN][1000 genomes]
rs62106626	1.00[ASN][1000 genomes]
rs62108934	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110063	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623196	1.00[ASN][1000 genomes]
rs636313	1.00[ASN][1000 genomes]
rs649239	1.00[ASN][1000 genomes]
rs6508931	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508932	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667850	1.00[ASN][1000 genomes]
rs7250244	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250298	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259136	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260610	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73551672	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73553618	1.00[ASN][1000 genomes]
rs8103746	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103807	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104932	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8105260	1.00[ASN][1000 genomes]
rs8108062	1.00[ASN][1000 genomes]
rs8108857	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
2	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv911697	chr19:40599603-40711333	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv3336591	chr19:40647161-40670363	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40647400-40654400	Enhancers	Primary T cells fromperipheralblood	blood
2	chr19:40648000-40654200	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr19:40648200-40654600	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr19:40648800-40655000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:40649800-40654400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:40650600-40654400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr19:40652800-40654200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr19:40653000-40654200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:40653000-40654600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr19:40653000-40654800	Enhancers	Primary hematopoietic stem cells	blood
11	chr19:40653200-40654200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:40653200-40654200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:40653200-40654200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr19:40653200-40654200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr19:40653200-40654200	Enhancers	Spleen	Spleen
16	chr19:40653200-40654200	Enhancers	HMEC	breast
17	chr19:40653200-40654200	Enhancers	HSMM	muscle
18	chr19:40653200-40654200	Enhancers	NHLF	lung
19	chr19:40653200-40654400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:40653200-40654400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr19:40653400-40654200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:40653400-40654200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:40653400-40654200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
24	chr19:40653400-40654200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr19:40653400-40654200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:40653400-40654200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:40653400-40654200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:40653400-40654200	Flanking Active TSS	Hela-S3	cervix
29	chr19:40653400-40654200	Enhancers	NH-A	brain
30	chr19:40653400-40654200	Flanking Active TSS	Osteobl	bone
31	chr19:40653400-40654400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:40653400-40654400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:40653400-40654400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:40653600-40654200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:40653600-40654400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:40653600-40654400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr19:40653600-40654400	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr19:40653600-40654400	Flanking Active TSS	NHEK	skin
39	chr19:40653800-40654200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:40653800-40654200	Active TSS	Brain Angular Gyrus	brain
41	chr19:40653800-40654200	Active TSS	Colonic Mucosa	Colon
42	chr19:40653800-40654200	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr19:40653800-40654200	Bivalent/Poised TSS	Placenta	Placenta
44	chr19:40653800-40654200	Active TSS	Rectal Smooth Muscle	rectum
45	chr19:40653800-40654200	Enhancers	Right Atrium	heart
46	chr19:40653800-40654200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
47	chr19:40654000-40654200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:40654000-40654200	Enhancers	Duodenum Mucosa	Duodenum
49	chr19:40654000-40654200	Enhancers	Left Ventricle	heart
50	chr19:40654000-40654200	Active TSS	A549	lung

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