Variant report

Variant	rs10164900
Chromosome Location	chr2:11214421-11214422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10174308	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10185403	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10221871	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10439232	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495579	1.00[YRI][hapmap]
rs11675414	0.80[EUR][1000 genomes]
rs11678376	1.00[YRI][hapmap]
rs11686282	0.91[AFR][1000 genomes]
rs13016104	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13019468	0.82[AFR][1000 genomes]
rs13021653	0.81[AFR][1000 genomes]
rs13032732	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13385775	0.91[AFR][1000 genomes]
rs13385890	0.91[AFR][1000 genomes]
rs13395933	0.91[AFR][1000 genomes]
rs13399692	1.00[YRI][hapmap]
rs71439047	0.91[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	nsv833392	chr2:11054580-11235239	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv580971	chr2:11175395-11226507	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10164900	GAGE12I	trans	lymphoblastoid	seeQTL
rs10164900	GAGE2C	trans	lymphoblastoid	seeQTL
rs10164900	GAGE4	trans	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11212600-11214600	Enhancers	Placenta	Placenta
2	chr2:11212600-11214600	Enhancers	HUVEC	blood vessel
3	chr2:11212800-11214800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:11213200-11214600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:11213400-11214600	Enhancers	Fetal Lung	lung
6	chr2:11213400-11214600	Enhancers	NHLF	lung
7	chr2:11213600-11214600	Enhancers	Fetal Stomach	stomach
8	chr2:11213800-11214600	Enhancers	NHDF-Ad	bronchial
9	chr2:11213800-11214800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:11213800-11215400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:11214200-11214800	Enhancers	Spleen	Spleen
12	chr2:11214400-11214600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:11214400-11214600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:11214400-11214600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:11214400-11219400	Weak transcription	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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