Variant report

Variant	rs2249296
Chromosome Location	chr1:86910264-86910265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11161820	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12564227	0.80[AMR][1000 genomes]
rs1334150	0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17129078	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2250857	0.92[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2252313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2791464	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2791465	0.87[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3765978	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4292929	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4393129	0.85[CHD][hapmap];0.82[GIH][hapmap]
rs4656108	0.85[ASN][1000 genomes]
rs61804060	0.81[EUR][1000 genomes]
rs9433030	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2249296	ODF2L	cis	multi-tissue	Pritchard
rs2249296	LOC339524	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86896600-86914400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:86897200-86922600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:86897200-86922800	Strong transcription	HMEC	breast
4	chr1:86897400-86916000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:86902000-86913200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:86903400-86926800	Weak transcription	Esophagus	oesophagus
7	chr1:86907600-86911600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:86908200-86911800	Weak transcription	Thymus	Thymus
9	chr1:86908800-86912400	Weak transcription	NHEK	skin
10	chr1:86909000-86911600	Weak transcription	Fetal Thymus	thymus
11	chr1:86909400-86910600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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