Variant report

Variant	rs1689059
Chromosome Location	chr21:17591602-17591603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11088579	0.87[EUR][1000 genomes]
rs12482948	0.88[EUR][1000 genomes]
rs1475883	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1475884	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1475885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492952	0.93[JPT][hapmap]
rs1626109	0.81[CHD][hapmap]
rs2823639	0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2823641	0.93[JPT][hapmap]
rs2823643	0.93[JPT][hapmap]
rs2823646	0.86[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap]
rs2823652	0.90[GIH][hapmap];0.82[TSI][hapmap]
rs2823657	0.91[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap]
rs2823658	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2823660	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2823661	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2823662	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2823674	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs62219537	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7276974	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs73364897	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs915799	0.93[JPT][hapmap]
rs9637000	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9978459	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066951	chr21:17458978-17603160	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv544381	chr21:17458978-17603160	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv432145	chr21:17559229-17628529	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv834051	chr21:17564843-17721764	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1689059	SAMSN1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17576000-17596800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:17584000-17598800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr21:17584200-17592200	Weak transcription	Fetal Muscle Leg	muscle
4	chr21:17584200-17592200	Weak transcription	Fetal Stomach	stomach
5	chr21:17584400-17596800	Weak transcription	Ovary	ovary
6	chr21:17584400-17619400	Weak transcription	Hela-S3	cervix
7	chr21:17584600-17596600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr21:17584600-17596600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr21:17585000-17592800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr21:17585000-17595200	Weak transcription	NHDF-Ad	bronchial
11	chr21:17585000-17612200	Weak transcription	Adipose Nuclei	Adipose
12	chr21:17585400-17595000	Weak transcription	Brain Angular Gyrus	brain
13	chr21:17585400-17604400	Weak transcription	Psoas Muscle	Psoas
14	chr21:17585800-17591800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr21:17586200-17596600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr21:17586200-17596800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr21:17588000-17593800	Weak transcription	Fetal Brain Male	brain
18	chr21:17588200-17592600	Weak transcription	Brain Anterior Caudate	brain
19	chr21:17588200-17595000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr21:17588600-17596600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr21:17588600-17600600	Weak transcription	Brain Hippocampus Middle	brain
22	chr21:17588800-17593200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr21:17588800-17594200	Weak transcription	Dnd41	blood
24	chr21:17588800-17595600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr21:17589000-17594400	Weak transcription	HUVEC	blood vessel
26	chr21:17589000-17597800	Weak transcription	Fetal Kidney	kidney
27	chr21:17589200-17595000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr21:17589600-17591800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr21:17589800-17596200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr21:17590200-17593200	Weak transcription	Fetal Heart	heart
31	chr21:17591000-17592000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr21:17591000-17592000	Enhancers	HepG2	liver
33	chr21:17591200-17598400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:17591600-17592000	Flanking Active TSS	Liver	Liver
35	chr21:17591600-17592400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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