Variant report

Variant	rs12462729
Chromosome Location	chr19:52666299-52666300
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12460375	0.84[ASN][1000 genomes]
rs12460432	0.84[ASN][1000 genomes]
rs12608745	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12609494	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12609518	0.87[CHB][hapmap]
rs12611170	0.94[CHB][hapmap]
rs12611229	0.83[ASN][1000 genomes]
rs17696575	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs17769264	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs28838074	0.83[ASN][1000 genomes]
rs35777966	0.83[ASN][1000 genomes]
rs35897677	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57312963	0.83[ASN][1000 genomes]
rs58547594	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61641512	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67664388	0.85[ASN][1000 genomes]
rs72626251	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv2762047	chr19:52647312-52668951	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv817856	chr19:52647893-52668697	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv580007	chr19:52660279-52693277	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52651600-52667200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:52653800-52670600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:52654000-52667200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:52654000-52669000	ZNF genes & repeats	Liver	Liver
5	chr19:52654400-52671600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:52654600-52669200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:52656200-52666400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:52656400-52669000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr19:52656400-52669200	ZNF genes & repeats	Primary T cells from cord blood	blood
10	chr19:52656600-52667000	ZNF genes & repeats	Fetal Brain Female	brain
11	chr19:52656600-52668200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
12	chr19:52656800-52666400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr19:52656800-52667200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
14	chr19:52656800-52669200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:52657000-52666400	ZNF genes & repeats	Dnd41	blood
16	chr19:52657000-52666600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:52659000-52667000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr19:52659000-52668600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:52659400-52671800	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr19:52659600-52669000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
21	chr19:52660000-52669200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr19:52660200-52666600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:52660400-52669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:52660600-52669000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:52661600-52669000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:52661600-52672200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:52661800-52666600	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr19:52661800-52667200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr19:52661800-52667200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
30	chr19:52661800-52669000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr19:52662000-52666400	ZNF genes & repeats	Aorta	Aorta
32	chr19:52662000-52667000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:52662000-52667000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
34	chr19:52662000-52667200	ZNF genes & repeats	Primary B cells from cord blood	blood
35	chr19:52662000-52667200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:52662000-52667200	ZNF genes & repeats	GM12878-XiMat	blood
37	chr19:52662000-52669000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr19:52662000-52669000	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr19:52662000-52669000	ZNF genes & repeats	Thymus	Thymus
40	chr19:52662000-52669200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr19:52662000-52669600	Strong transcription	Brain Anterior Caudate	brain
42	chr19:52662000-52671600	Strong transcription	Brain Angular Gyrus	brain
43	chr19:52662000-52672200	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:52662200-52667200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:52662200-52669000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:52662200-52669000	Strong transcription	Brain Hippocampus Middle	brain
47	chr19:52662400-52669000	Strong transcription	Colonic Mucosa	Colon
48	chr19:52662400-52669000	Strong transcription	Pancreas	Pancrea
49	chr19:52662400-52669200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:52662600-52666400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin

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