Variant report

Variant	rs1400590
Chromosome Location	chr12:118026527-118026528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10774936	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774937	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850846	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850847	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850848	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850851	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850854	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850855	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068565	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308267	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369419	1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61938965	0.82[EUR][1000 genomes];1.00[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	nsv832527	chr12:117974007-118110244	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1400590	KSR2	cis	parietal	SCAN
rs1400590	OAS3	cis	cerebellum	SCAN
rs1400590	MED13L	cis	parietal	SCAN
rs1400590	MED13L	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118021800-118036800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:118025400-118026600	Enhancers	A549	lung
3	chr12:118025400-118030800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:118025600-118027000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:118025600-118030800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:118025600-118030800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:118026400-118026600	Enhancers	Liver	Liver

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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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