Variant report

Variant	rs2020009
Chromosome Location	chr4:152837454-152837455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs165578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs360918	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs360922	1.00[ASN][1000 genomes]
rs360936	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs360937	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs360951	0.81[MEX][hapmap]
rs361131	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs499797	0.80[AMR][1000 genomes]
rs511880	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs518213	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs530315	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2020009	FGG	cis	cerebellum	SCAN
rs2020009	ANXA2P1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152831600-152838400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr4:152833600-152838200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:152834000-152838800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:152834200-152838400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:152834200-152838600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:152836200-152851000	Weak transcription	Fetal Thymus	thymus

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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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