Variant report

Variant	rs2650773
Chromosome Location	chr19:21644088-21644089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12974758	0.82[ASN][1000 genomes]
rs2562428	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2562456	0.83[ASN][1000 genomes]
rs2562474	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2562487	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2650764	0.83[ASN][1000 genomes]
rs2650784	0.83[ASN][1000 genomes]
rs2650793	0.80[ASN][1000 genomes]
rs2650801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2650804	0.80[ASN][1000 genomes]
rs2650805	0.82[ASN][1000 genomes]
rs2650814	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914646	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928211	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2968072	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2968076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516519	0.85[EUR][1000 genomes]
rs56072098	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs627522	0.85[EUR][1000 genomes]
rs6511250	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6511253	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6511254	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7252585	0.83[ASN][1000 genomes]
rs8106025	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304986	0.80[ASN][1000 genomes]
rs9304987	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers 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 target site	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv961284	chr19:21636687-21659271	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2650773	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs2650773	ZNF708	cis	lung	GTEx
rs2650773	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs2650773	CTD-2561J22.5	cis	Thyroid	GTEx
rs2650773	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2650773	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs2650773	ZNF708	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21636800-21645800	Weak transcription	Fetal Kidney	kidney
2	chr19:21636800-21646200	Weak transcription	Fetal Heart	heart
3	chr19:21639400-21645600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:21639600-21646000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:21640600-21644200	ZNF genes & repeats	Ovary	ovary
6	chr19:21641000-21645800	Weak transcription	Thymus	Thymus
7	chr19:21641200-21644200	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr19:21641200-21645200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:21641200-21645200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:21641200-21646000	Weak transcription	Fetal Lung	lung
11	chr19:21641200-21646400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:21642600-21646800	Active TSS	K562	blood
13	chr19:21643000-21644200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:21643200-21644400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:21643400-21644200	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr19:21643400-21645000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:21643400-21645600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:21643400-21645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:21643600-21644200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:21643600-21645800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:21643800-21644600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:21643800-21644600	Strong transcription	Dnd41	blood
23	chr19:21643800-21644800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:21643800-21645000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:21643800-21645200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:21643800-21645400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:21643800-21645600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr19:21643800-21645600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:21643800-21645600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:21643800-21646000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr19:21644000-21644200	Enhancers	Placenta	Placenta
32	chr19:21644000-21645600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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