Variant report

Variant	rs17273442
Chromosome Location	chr19:57022744-57022745
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10404464	0.85[EUR][1000 genomes]
rs10406513	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10406535	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10406985	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10408108	0.86[EUR][1000 genomes]
rs10414817	0.86[EUR][1000 genomes]
rs10415223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10416884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417966	0.87[EUR][1000 genomes]
rs10419553	0.87[EUR][1000 genomes]
rs10419939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422306	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973457	0.83[EUR][1000 genomes]
rs12981768	0.85[EUR][1000 genomes]
rs12984487	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2058132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2189698	0.86[EUR][1000 genomes]
rs2286423	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35780595	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106523	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8106788	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958338	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs960995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs993510	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv912519	chr19:57020754-57065189	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57020200-57024200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:57020200-57025400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:57020200-57025400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr19:57020200-57025600	Weak transcription	Left Ventricle	heart
5	chr19:57020200-57025800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:57020200-57027200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:57020200-57029800	Weak transcription	Gastric	stomach
8	chr19:57020400-57022800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:57020400-57022800	Weak transcription	Brain Hippocampus Middle	brain
10	chr19:57020400-57022800	Weak transcription	Brain Substantia Nigra	brain
11	chr19:57020400-57022800	Weak transcription	Ovary	ovary
12	chr19:57020400-57022800	Weak transcription	NHDF-Ad	bronchial
13	chr19:57020400-57023000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:57020400-57024400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:57020400-57024600	Weak transcription	Fetal Heart	heart
16	chr19:57020400-57024600	Weak transcription	HSMMtube	muscle
17	chr19:57020400-57025200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr19:57020400-57025400	Weak transcription	Fetal Muscle Leg	muscle
19	chr19:57020400-57025600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:57020400-57027600	Weak transcription	Osteobl	bone
21	chr19:57020400-57030400	Weak transcription	Right Ventricle	heart
22	chr19:57020600-57022800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr19:57020600-57023800	Weak transcription	Placenta	Placenta
24	chr19:57020600-57024200	Weak transcription	Brain Angular Gyrus	brain
25	chr19:57020600-57025600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:57020600-57025600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:57020600-57025600	Weak transcription	Brain Anterior Caudate	brain
28	chr19:57020600-57028800	Weak transcription	Fetal Stomach	stomach
29	chr19:57020800-57024400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr19:57021000-57022800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:57021000-57027400	Weak transcription	HSMM	muscle
32	chr19:57021200-57026000	Weak transcription	Fetal Brain Female	brain
33	chr19:57021400-57026000	Weak transcription	Fetal Brain Male	brain
34	chr19:57021400-57027400	Weak transcription	Brain Germinal Matrix	brain
35	chr19:57021800-57023000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:57021800-57024400	Weak transcription	Fetal Kidney	kidney
37	chr19:57022000-57024000	Weak transcription	Adipose Nuclei	Adipose
38	chr19:57022000-57025400	Weak transcription	Aorta	Aorta
39	chr19:57022200-57024400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr19:57022200-57025800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:57022400-57025800	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:57022600-57023400	ZNF genes & repeats	Psoas Muscle	Psoas
43	chr19:57022600-57042800	ZNF genes & repeats	Liver	Liver

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