Variant report

Variant	rs2970052
Chromosome Location	chr17:50224898-50224899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1393730	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1503045	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1503046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2036483	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2970049	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[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	nsv492317	chr17:50067819-50774475	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2970052	CDC27	cis	parietal	SCAN
rs2970052	ZNF652	cis	cerebellum	SCAN
rs2970052	HOXB13	cis	parietal	SCAN
rs2970052	MYL4	cis	parietal	SCAN
rs2970052	NME1	cis	parietal	SCAN
rs2970052	CACNA1G	cis	cerebellum	SCAN
rs2970052	WNT3	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:50221000-50228200	Enhancers	NHEK	skin
2	chr17:50222000-50228000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr17:50222200-50227800	Enhancers	HMEC	breast
4	chr17:50222400-50228000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:50222600-50227600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:50223000-50225200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr17:50223400-50225000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr17:50223400-50225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:50224000-50228000	Enhancers	Hela-S3	cervix
10	chr17:50224400-50225000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr17:50224400-50225200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:50224400-50225200	Weak transcription	Fetal Muscle Leg	muscle
13	chr17:50224600-50226800	Enhancers	NH-A	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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