Variant report

Variant	rs920590
Chromosome Location	chr8:19651161-19651162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10090638	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs11204077	0.93[YRI][hapmap];0.92[AFR][1000 genomes]
rs11777075	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2083640	0.83[AFR][1000 genomes]
rs2083641	0.81[AFR][1000 genomes]
rs3855754	0.87[AFR][1000 genomes]
rs3866469	0.91[AFR][1000 genomes]
rs4398935	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4922099	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58556504	0.83[AFR][1000 genomes]
rs6586867	0.93[AFR][1000 genomes]
rs67391684	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6982084	0.88[ASW][hapmap];0.92[LWK][hapmap]
rs6995371	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7012694	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv610759	chr8:19561997-20068842	Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv890629	chr8:19625038-19665351	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1032405	chr8:19634973-19658017	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv890630	chr8:19635098-19658912	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv526671	chr8:19643614-19655319	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Acute lymphoblastic leukemia (childhood)	22076464	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs920590	INTS10	cis	parietal	SCAN
rs920590	NAT1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19650600-19652400	Enhancers	Fetal Lung	lung
2	chr8:19651000-19651200	Enhancers	NHDF-Ad	bronchial
3	chr8:19651000-19651600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr8:19651000-19651600	Enhancers	Fetal Muscle Leg	muscle

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Input of quick search could be:

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

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