Variant report

Variant	rs2801536
Chromosome Location	chr10:90853352-90853353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10509563	0.90[GIH][hapmap];0.95[MEX][hapmap]
rs2000360	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2247755	0.95[CEU][hapmap]
rs2252139	0.80[AMR][1000 genomes]
rs2253515	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2255465	0.80[AMR][1000 genomes]
rs2494643	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2801522	0.89[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs2801533	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2801539	0.80[AMR][1000 genomes]
rs2841019	0.87[EUR][1000 genomes]
rs2841021	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2841024	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2841032	0.85[EUR][1000 genomes]
rs7076595	0.85[EUR][1000 genomes]
rs9421696	0.83[EUR][1000 genomes]
rs9651494	0.96[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv467416	chr10:90815975-90889997	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv551842	chr10:90815975-90889997	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv895880	chr10:90816060-90874029	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv831944	chr10:90822654-90967018	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv467418	chr10:90826252-90874468	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv551843	chr10:90826252-90874468	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv2829934	chr10:90826779-90874468	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2758235	chr10:90835064-91017486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2759775	chr10:90835064-91017486	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv895881	chr10:90842431-90940003	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2801536	IFIT5	cis	cerebellum	SCAN
rs2801536	KIF11	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90841800-90861000	Weak transcription	Aorta	Aorta
2	chr10:90845200-90855000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:90847400-90859200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:90850600-90854200	Enhancers	NHDF-Ad	bronchial
5	chr10:90852000-90859200	Weak transcription	Ovary	ovary
6	chr10:90852400-90853600	Enhancers	Fetal Thymus	thymus
7	chr10:90852800-90853800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:90853000-90854000	Enhancers	Osteobl	bone

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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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