Variant report

Variant	rs10496623
Chromosome Location	chr2:124870012-124870013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10496625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12614779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622072	1.00[ASW][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs1371147	1.00[YRI][hapmap]
rs17010780	1.00[YRI][hapmap]
rs17010809	1.00[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17010810	1.00[YRI][hapmap]
rs17010817	1.00[ASW][hapmap];0.80[CHD][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs17010819	1.00[YRI][hapmap]
rs17010881	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17010934	1.00[ASW][hapmap]
rs17010944	1.00[YRI][hapmap]
rs2699381	1.00[ASW][hapmap]
rs4848911	1.00[YRI][hapmap]
rs4848916	1.00[ASW][hapmap]
rs55718116	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7585692	1.00[YRI][hapmap]
rs7591828	0.88[EUR][1000 genomes];0.81[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	nsv531408	chr2:124727329-125011247	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10496623	SNORD99	trans	lymphoblastoid	seeQTL
rs10496623	SNORD50A	trans	lymphoblastoid	seeQTL
rs10496623	SNORD116-29	trans	lymphoblastoid	seeQTL
rs10496623	SNORD41	trans	lymphoblastoid	seeQTL
rs10496623	SNORD78	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:124867600-124870400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:124868400-124870200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:124868600-124870400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:124868800-124870200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:124869600-124870400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:124869600-124870400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:124869600-124870600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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