Variant report

Variant	rs17207495
Chromosome Location	chr19:57028079-57028080
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10403034	0.83[EUR][1000 genomes]
rs10405130	0.85[EUR][1000 genomes]
rs10405534	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407163	0.83[EUR][1000 genomes]
rs10408508	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413931	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415931	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417351	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418635	0.87[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422564	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13346710	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2058131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286420	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34136271	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3752177	0.83[EUR][1000 genomes]
rs73055319	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73055321	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068034	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068037	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068061	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070034	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070060	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070074	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070077	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73070080	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
13	nsv580387	chr19:57026396-57040070	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17207495	TRIM28	cis	cerebellum	SCAN
rs17207495	ZNF418	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57020200-57029800	Weak transcription	Gastric	stomach
2	chr19:57020400-57030400	Weak transcription	Right Ventricle	heart
3	chr19:57020600-57028800	Weak transcription	Fetal Stomach	stomach
4	chr19:57022600-57042800	ZNF genes & repeats	Liver	Liver
5	chr19:57022800-57031200	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr19:57022800-57049200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:57023000-57037400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:57023400-57029800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr19:57023800-57028200	Strong transcription	Placenta	Placenta
10	chr19:57023800-57028400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:57023800-57028400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:57024200-57028400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr19:57024200-57030400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:57024400-57028600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr19:57024400-57038800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:57025400-57028400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
17	chr19:57025400-57029600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:57025600-57028200	Strong transcription	Brain Cingulate Gyrus	brain
19	chr19:57025600-57028400	ZNF genes & repeats	Brain Substantia Nigra	brain
20	chr19:57025600-57028400	Strong transcription	Stomach Smooth Muscle	stomach
21	chr19:57025600-57028600	ZNF genes & repeats	Brain Anterior Caudate	brain
22	chr19:57025600-57038200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:57025600-57049200	ZNF genes & repeats	Adipose Nuclei	Adipose
24	chr19:57025800-57028400	ZNF genes & repeats	Fetal Kidney	kidney
25	chr19:57025800-57030600	Weak transcription	Pancreas	Pancrea
26	chr19:57025800-57031200	Weak transcription	Esophagus	oesophagus
27	chr19:57026000-57040200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
28	chr19:57026200-57029600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:57026200-57031400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:57026600-57028400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr19:57027000-57029800	Weak transcription	Fetal Brain Male	brain
32	chr19:57027200-57028200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr19:57027200-57028200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
34	chr19:57027200-57028400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:57027200-57035800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
36	chr19:57027200-57038600	ZNF genes & repeats	Ovary	ovary
37	chr19:57027400-57028200	ZNF genes & repeats	Brain Angular Gyrus	brain
38	chr19:57027400-57028400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:57027400-57028400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
40	chr19:57027400-57028400	ZNF genes & repeats	Fetal Brain Female	brain
41	chr19:57027400-57034400	ZNF genes & repeats	Fetal Lung	lung
42	chr19:57027400-57040800	ZNF genes & repeats	Brain Hippocampus Middle	brain
43	chr19:57027600-57028200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:57027600-57028200	ZNF genes & repeats	Brain Germinal Matrix	brain
45	chr19:57027600-57028400	ZNF genes & repeats	Primary T cells from cord blood	blood
46	chr19:57027800-57028400	Strong transcription	HSMM	muscle
47	chr19:57027800-57029400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr19:57027800-57029600	Weak transcription	Osteobl	bone
49	chr19:57028000-57028200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:57028000-57028200	Weak transcription	Left Ventricle	heart

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