Variant report

Variant	rs62108312
Chromosome Location	chr19:52868315-52868316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52861409..52864151-chr19:52865571..52868442,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10401360	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419807	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1120184	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11666043	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666131	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11667184	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670904	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11881435	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2115102	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2247987	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2263899	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2263901	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2434418	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2434460	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2560883	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2560885	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2560968	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2560990	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2560991	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2657937	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2657938	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2657939	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2657940	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2903978	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903979	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35017258	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59043312	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62108276	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108308	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108309	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62108312	ZNF480	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
4	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:52856800-52870200	ZNF genes & repeats	Ovary	ovary
6	chr19:52858800-52871800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:52859600-52868800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:52861800-52872200	ZNF genes & repeats	Fetal Lung	lung
9	chr19:52862000-52870200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr19:52862000-52871000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:52862000-52871000	ZNF genes & repeats	Fetal Brain Female	brain
12	chr19:52862000-52871200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:52862600-52871400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:52862800-52870600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
15	chr19:52863000-52868600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:52864200-52870600	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr19:52865200-52870200	ZNF genes & repeats	Fetal Intestine Large	intestine
18	chr19:52865200-52871200	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr19:52865200-52875400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:52865600-52871200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:52866000-52871200	ZNF genes & repeats	Dnd41	blood
22	chr19:52866400-52870400	ZNF genes & repeats	Brain Hippocampus Middle	brain
23	chr19:52866600-52870200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
24	chr19:52866600-52870200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
25	chr19:52866600-52872200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:52866600-52875400	ZNF genes & repeats	Liver	Liver
27	chr19:52866800-52869800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
28	chr19:52866800-52870200	ZNF genes & repeats	Brain Anterior Caudate	brain
29	chr19:52866800-52871200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr19:52866800-52871200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:52867200-52868400	Weak transcription	Brain Substantia Nigra	brain
32	chr19:52867200-52868600	Weak transcription	Brain Angular Gyrus	brain
33	chr19:52867200-52868600	Weak transcription	Fetal Heart	heart
34	chr19:52867200-52872400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
35	chr19:52867400-52868400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:52867600-52870000	ZNF genes & repeats	Fetal Stomach	stomach
37	chr19:52867600-52871000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
38	chr19:52867600-52871200	ZNF genes & repeats	Fetal Muscle Leg	muscle
39	chr19:52867600-52872200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr19:52867800-52869600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:52867800-52869800	ZNF genes & repeats	Lung	lung
42	chr19:52867800-52870000	ZNF genes & repeats	Aorta	Aorta
43	chr19:52867800-52870000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:52867800-52870000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
45	chr19:52867800-52870000	ZNF genes & repeats	Fetal Brain Male	brain
46	chr19:52867800-52870200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
47	chr19:52867800-52870200	ZNF genes & repeats	Left Ventricle	heart
48	chr19:52867800-52870600	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr19:52867800-52871400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:52867800-52872200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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