Variant report

Variant	rs10992028
Chromosome Location	chr9:94406034-94406035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10820880	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10991995	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10992000	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992004	1.00[YRI][hapmap]
rs10992005	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992009	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12554309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12555698	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17584241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744068	0.92[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs72742884	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72744404	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72744408	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][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	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv818713	chr9:94396059-94406084	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992028	PHF2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94405200-94406600	Enhancers	Fetal Stomach	stomach
2	chr9:94405200-94406600	Enhancers	GM12878-XiMat	blood
3	chr9:94405400-94406400	Enhancers	Stomach Smooth Muscle	stomach
4	chr9:94405800-94406600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:94406000-94406800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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