Variant report

Variant	rs165579
Chromosome Location	chr4:152861685-152861686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs171507	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs360913	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs360916	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs360917	0.85[AMR][1000 genomes]
rs360950	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs360951	0.88[GIH][hapmap]
rs360954	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1030328	chr4:152791533-152875666	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1028836	chr4:152791680-152879097	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs165579	NR3C2	cis	parietal	SCAN
rs165579	FGG	cis	cerebellum	SCAN
rs165579	SFRP2	cis	parietal	SCAN
rs165579	FBXW7	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152860200-152862800	Enhancers	Fetal Thymus	thymus
2	chr4:152860800-152862800	Enhancers	Thymus	Thymus
3	chr4:152860800-152863000	Enhancers	Dnd41	blood
4	chr4:152861200-152862200	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr4:152861400-152862600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:152861400-152862600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr4:152861400-152862800	Enhancers	HMEC	breast
8	chr4:152861600-152862000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:152861600-152862600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr4:152861600-152862600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:152861600-152862600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr4:152861600-152862800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:152861600-152862800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr4:152861600-152862800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr4:152861600-152862800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:152861600-152862800	Enhancers	NHEK	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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