Variant report

Variant	rs4743993
Chromosome Location	chr9:98102983-98102984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1027710	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739992	0.96[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs10761382	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761387	0.81[EUR][1000 genomes]
rs10821455	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs10821458	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10821459	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821461	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821462	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10993518	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1979022	0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs2031599	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs2036516	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2166402	0.96[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs2297596	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs2297597	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.80[TSI][hapmap]
rs3277	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs35081772	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3737142	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs3780568	0.96[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs3844341	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs3852402	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs4647382	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4647459	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs4647462	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs4647475	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs4744446	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs4744451	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs4744454	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744459	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7019043	0.82[EUR][1000 genomes]
rs7026047	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027204	0.92[CEU][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7034538	0.82[CEU][hapmap];0.87[JPT][hapmap]
rs7850958	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs7854570	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs7858493	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs963774	0.92[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap]

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	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv3330996	chr9:98083446-98112507	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4743993	PHF2	cis	cerebellum	SCAN
rs4743993	HABP4	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98099600-98105000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:98101000-98105000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:98102600-98104200	Enhancers	Fetal Lung	lung

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