Variant report

Variant	rs2142907
Chromosome Location	chr1:210039505-210039506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10863793	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1108628	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119357	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12022221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883331	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963685	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964106	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049999	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2357231	0.82[ASN][1000 genomes]
rs4133950	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7537294	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542091	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7548545	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550330	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550733	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429825	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9429826	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2142907	SYT14	cis	Nerve Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210017600-210041200	Weak transcription	Fetal Brain Male	brain
2	chr1:210028200-210042400	Weak transcription	NHDF-Ad	bronchial
3	chr1:210028400-210039600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:210037000-210042400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:210037200-210041800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:210037200-210041800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:210037200-210042400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:210037400-210041800	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:210037400-210042400	Weak transcription	Fetal Lung	lung
10	chr1:210037600-210041000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:210037600-210042200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:210037600-210042200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:210037600-210042400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:210038000-210042200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:210038000-210043200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:210038000-210044000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:210038000-210044600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:210038000-210048800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:210038600-210042600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:210038600-210042800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:210039400-210039800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:210039400-210040000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:210039400-210040200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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