Variant report

Variant	rs407096
Chromosome Location	chr19:42512281-42512282
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	chr19:42502921..42504612-chr19:42510265..42512781,2	K562	blood:
2	chr19:42505192..42506828-chr19:42511615..42513645,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP1A3-1	chr19:42511266-42512300	ENSG00000250528

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16975663	0.89[AFR][1000 genomes]
rs3736109	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs443239	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454150	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803520	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251466	0.83[EUR][1000 genomes]
rs899661	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs407096	ZNF219	trans	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42504800-42532600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:42505000-42534200	Weak transcription	Fetal Brain Male	brain
3	chr19:42505200-42525000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr19:42506000-42525400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr19:42506000-42529000	Weak transcription	Brain Angular Gyrus	brain
6	chr19:42506000-42535400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:42506600-42523800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:42507200-42513000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:42507600-42528200	Weak transcription	Colon Smooth Muscle	Colon
10	chr19:42508000-42513000	Weak transcription	Dnd41	blood
11	chr19:42508200-42524800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr19:42508400-42525600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr19:42508600-42513200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:42508600-42524600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:42508600-42527200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:42510000-42522600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr19:42510000-42528800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:42510200-42525200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:42510800-42525200	Weak transcription	Brain Anterior Caudate	brain
20	chr19:42511000-42520800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:42511000-42525200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr19:42511000-42525600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:42511000-42528600	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:42511000-42542600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:42511200-42519600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:42511200-42520600	Weak transcription	Fetal Stomach	stomach
27	chr19:42511200-42525200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:42511200-42532600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:42511800-42519600	Weak transcription	Brain Germinal Matrix	brain
30	chr19:42511800-42522800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:42511800-42523400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:42511800-42525200	Weak transcription	Aorta	Aorta
33	chr19:42512000-42519600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:42512000-42519800	Weak transcription	Fetal Brain Female	brain

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