Variant report

Variant	rs204548
Chromosome Location	chr19:44947050-44947051
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	chr19:44945678..44948451-chr19:44948958..44951509,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF229-1	chr19:44947012-44947208	ENSG00000267188.1
2	lnc-ZNF229-1	chr19:44946998-44947208	NONHSAT066697

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1734622	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865385	1.00[ASN][1000 genomes]
rs204527	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204529	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204530	1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204532	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204542	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204553	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204554	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs204556	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2571041	1.00[ASN][1000 genomes]
rs2571053	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2571059	1.00[ASN][1000 genomes]
rs2686756	1.00[ASN][1000 genomes]
rs2686757	1.00[ASN][1000 genomes]
rs2686769	1.00[ASN][1000 genomes]
rs431273	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62118147	1.00[ASN][1000 genomes]
rs629579	1.00[ASN][1000 genomes]
rs8107008	1.00[CHB][hapmap]
rs8110499	0.89[EUR][1000 genomes]
rs930462	1.00[CHB][hapmap]
rs954314	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers 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	18 gene(s)	inside rSNPs	diseases
4	esv2756827	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2758764	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs204548	ZNF180	cis	Muscle Skeletal	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44928400-44951800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:44932000-44953200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr19:44934600-44950800	Weak transcription	Hela-S3	cervix
4	chr19:44936000-44951400	Weak transcription	Fetal Heart	heart
5	chr19:44936400-44952000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:44937400-44951800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:44938400-44951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:44938800-44951600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:44939000-44948400	Weak transcription	NHEK	skin
10	chr19:44940000-44948200	Weak transcription	Osteobl	bone
11	chr19:44940000-44950600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:44940200-44951200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr19:44940600-44951800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:44940600-44951800	Weak transcription	Fetal Thymus	thymus
15	chr19:44941600-44950400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:44942000-44950200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:44942000-44950400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:44942000-44950800	ZNF genes & repeats	Fetal Brain Female	brain
19	chr19:44942200-44951800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:44942400-44950400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
21	chr19:44942400-44951400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:44942600-44952000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:44943000-44947200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:44944200-44947800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:44944200-44950400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:44944400-44949800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:44944400-44952200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
28	chr19:44944600-44949600	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:44944600-44952200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:44944800-44948400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:44945000-44948400	Weak transcription	Brain Angular Gyrus	brain
32	chr19:44945000-44949600	ZNF genes & repeats	Fetal Muscle Leg	muscle
33	chr19:44945000-44951200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
34	chr19:44945200-44947400	ZNF genes & repeats	Primary B cells from cord blood	blood
35	chr19:44945200-44951200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:44945400-44950600	Strong transcription	HMEC	breast
37	chr19:44945400-44951200	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr19:44945600-44951800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:44945800-44948200	Strong transcription	A549	lung
40	chr19:44945800-44950400	ZNF genes & repeats	Adipose Nuclei	Adipose
41	chr19:44945800-44951000	Strong transcription	NHLF	lung
42	chr19:44946000-44947200	ZNF genes & repeats	Brain Anterior Caudate	brain
43	chr19:44946000-44947400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:44946000-44947400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:44946000-44947400	Strong transcription	NH-A	brain
46	chr19:44946000-44947600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:44946000-44948800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:44946000-44949200	ZNF genes & repeats	Brain Hippocampus Middle	brain
49	chr19:44946000-44950600	ZNF genes & repeats	Ovary	ovary
50	chr19:44946200-44947400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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