Variant report

Variant	rs2496433
Chromosome Location	chr13:39280617-39280618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11147723	0.87[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11147724	0.87[CEU][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs11147725	0.87[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2442366	0.91[YRI][hapmap]
rs2442373	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2496418	0.80[ASN][1000 genomes]
rs2496419	0.80[ASN][1000 genomes]
rs2496420	0.87[CEU][hapmap];0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2496430	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2496434	0.81[AFR][1000 genomes]
rs2496437	0.81[AFR][1000 genomes]
rs55860060	0.83[AMR][1000 genomes]
rs55880170	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922882	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9634754	0.86[JPT][hapmap]
rs9788341	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs990909	0.81[AFR][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	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2496433	CSNK1A1L	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39265800-39287200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:39268000-39284600	Weak transcription	Fetal Kidney	kidney
3	chr13:39268200-39282400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:39276400-39286800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr13:39277000-39283800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:39277200-39286800	Weak transcription	Fetal Lung	lung
7	chr13:39277800-39281600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr13:39277800-39281600	Weak transcription	Brain Germinal Matrix	brain
9	chr13:39279200-39294600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr13:39280000-39281400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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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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