Variant report

Variant	rs11673497
Chromosome Location	chr19:38169655-38169656
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF781-2	chr19:38169524-38169674	NONHSAT066153

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1060522	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10853710	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11083429	0.82[EUR][1000 genomes]
rs11083433	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11666172	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11668796	1.00[EUR][1000 genomes]
rs11671953	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975299	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17246792	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28431170	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891657	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34991303	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55871826	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55913702	1.00[EUR][1000 genomes]
rs55950325	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62108305	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62108351	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6508739	1.00[EUR][1000 genomes]
rs7249622	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7253081	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7258385	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73037060	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102818	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11673497	ZNF573	cis	multi-tissue	Pritchard
rs11673497	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38166600-38182600	Weak transcription	Right Ventricle	heart
2	chr19:38166800-38171400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:38166800-38180000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:38167000-38170400	ZNF genes & repeats	Liver	Liver
5	chr19:38167000-38171400	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:38167400-38170600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
7	chr19:38167400-38171600	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:38167600-38170400	ZNF genes & repeats	Brain Angular Gyrus	brain
9	chr19:38167600-38170400	ZNF genes & repeats	Brain Hippocampus Middle	brain
10	chr19:38168600-38170400	ZNF genes & repeats	Fetal Lung	lung
11	chr19:38168600-38170400	ZNF genes & repeats	Dnd41	blood
12	chr19:38168600-38171400	ZNF genes & repeats	Aorta	Aorta
13	chr19:38168600-38171600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
14	chr19:38168600-38171600	ZNF genes & repeats	Brain Germinal Matrix	brain
15	chr19:38168800-38170000	ZNF genes & repeats	Spleen	Spleen
16	chr19:38168800-38170200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
17	chr19:38168800-38171400	ZNF genes & repeats	Left Ventricle	heart
18	chr19:38168800-38172200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:38168800-38172600	ZNF genes & repeats	Fetal Stomach	stomach
20	chr19:38169000-38169800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:38169000-38170600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:38169200-38170000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:38169200-38170400	ZNF genes & repeats	Brain Substantia Nigra	brain
24	chr19:38169200-38170400	ZNF genes & repeats	Ovary	ovary
25	chr19:38169400-38170400	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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