Variant report

Variant	rs7282349
Chromosome Location	chr21:16564561-16564562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11088317	1.00[CHB][hapmap]
rs11909473	0.84[ASN][1000 genomes]
rs2205439	1.00[JPT][hapmap]
rs2403907	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2823125	1.00[JPT][hapmap]
rs2823128	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823131	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823132	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823133	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823134	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2823135	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823136	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2823137	0.80[CHB][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs7275438	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275695	0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276622	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs926167	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv1063385	chr21:16521617-16926212	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv913413	chr21:16537728-16621859	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7282349	TSSC4	trans	parietal	SCAN
rs7282349	C21orf91	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16556600-16568000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:16563400-16564800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr21:16564200-16564800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr21:16564200-16564800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr21:16564200-16564800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr21:16564200-16564800	Enhancers	Fetal Intestine Large	intestine
7	chr21:16564200-16564800	Enhancers	Hela-S3	cervix
8	chr21:16564400-16564800	Enhancers	A549	lung
9	chr21:16564400-16565000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr21:16564400-16565000	Enhancers	HMEC	breast
11	chr21:16564400-16565000	Enhancers	NHEK	skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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