Variant report

Variant	rs7198449
Chromosome Location	chr16:72389230-72389231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10153187	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10492821	0.88[ASN][1000 genomes]
rs10492822	0.88[ASN][1000 genomes]
rs12325146	0.86[ASN][1000 genomes]
rs12325151	0.86[ASN][1000 genomes]
rs1297137	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1429071	0.93[ASN][1000 genomes]
rs16970855	0.80[AFR][1000 genomes]
rs16970933	0.88[ASN][1000 genomes]
rs17607347	0.89[AFR][1000 genomes]
rs17608394	0.94[ASN][1000 genomes]
rs17608557	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs17609544	0.86[ASN][1000 genomes]
rs17609577	0.86[ASN][1000 genomes]
rs17609787	0.85[ASN][1000 genomes]
rs17609808	0.84[ASN][1000 genomes]
rs17669912	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17676691	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17676709	0.94[ASN][1000 genomes]
rs17677146	0.88[ASN][1000 genomes]
rs17677484	0.86[ASN][1000 genomes]
rs17677616	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs17677890	0.85[ASN][1000 genomes]
rs2262554	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2336437	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs55808336	0.85[ASN][1000 genomes]
rs56348767	0.83[ASN][1000 genomes]
rs56389222	0.86[ASN][1000 genomes]
rs57220817	0.82[ASN][1000 genomes]
rs57755001	0.84[ASN][1000 genomes]
rs58549165	0.84[ASN][1000 genomes]
rs58745414	0.84[ASN][1000 genomes]
rs58860566	0.85[ASN][1000 genomes]
rs59966262	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60502114	0.86[ASN][1000 genomes]
rs60731174	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60855478	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61475520	0.85[ASN][1000 genomes]
rs62051129	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs62051130	0.93[ASN][1000 genomes]
rs62051131	0.93[ASN][1000 genomes]
rs62051136	0.88[ASN][1000 genomes]
rs62051137	0.88[ASN][1000 genomes]
rs62051145	0.84[ASN][1000 genomes]
rs62051146	0.84[ASN][1000 genomes]
rs62051147	0.84[ASN][1000 genomes]
rs62051148	0.85[ASN][1000 genomes]
rs62051149	0.84[ASN][1000 genomes]
rs62051150	0.83[ASN][1000 genomes]
rs62051151	0.83[ASN][1000 genomes]
rs62052871	0.84[ASN][1000 genomes]
rs62052877	0.86[ASN][1000 genomes]
rs62052878	0.86[ASN][1000 genomes]
rs62052879	0.85[ASN][1000 genomes]
rs62052881	0.85[ASN][1000 genomes]
rs62052888	0.85[ASN][1000 genomes]
rs62052890	0.85[ASN][1000 genomes]
rs62052891	0.85[ASN][1000 genomes]
rs62052895	0.84[ASN][1000 genomes]
rs62052909	0.85[ASN][1000 genomes]
rs62052911	0.85[ASN][1000 genomes]
rs62052915	0.83[ASN][1000 genomes]
rs62053965	0.81[ASN][1000 genomes]
rs62053966	0.86[ASN][1000 genomes]
rs62053968	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62053991	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62053992	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62053995	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62053996	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62053997	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62053998	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7193177	0.85[ASN][1000 genomes]
rs7194024	0.88[ASN][1000 genomes]
rs7195825	0.88[ASN][1000 genomes]
rs7197154	0.85[ASN][1000 genomes]
rs7199954	0.88[ASN][1000 genomes]
rs7200367	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7200814	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7204260	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7205716	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7206298	0.90[ASN][1000 genomes]
rs72791149	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72793244	0.85[ASN][1000 genomes]
rs72793252	0.85[ASN][1000 genomes]
rs72793263	0.84[ASN][1000 genomes]
rs8047074	0.81[ASN][1000 genomes]
rs8056067	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8058832	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8063172	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs806732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs806738	0.93[ASN][1000 genomes]
rs806747	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1063172	chr16:72342110-72537808	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv542947	chr16:72342110-72537808	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1067525	chr16:72342110-72602796	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv542948	chr16:72342110-72602796	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1867	chr16:72352262-72397339	Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
10	nsv1057127	chr16:72375524-72509686	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv542949	chr16:72375524-72509686	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	esv3348591	chr16:72387854-72389785	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7198449	PLEKHG4	cis	parietal	SCAN
rs7198449	PHLPP2	cis	cerebellum	SCAN
rs7198449	CYB5B	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72367200-72405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:72367200-72423600	Weak transcription	Thymus	Thymus
3	chr16:72370200-72399600	Weak transcription	Primary B cells from cord blood	blood
4	chr16:72388400-72389800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr16:72388600-72389600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr16:72389000-72389600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr16:72389200-72389600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:72389200-72389600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr16:72389200-72389600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr16:72389200-72389600	Enhancers	Aorta	Aorta
11	chr16:72389200-72390000	Enhancers	Osteobl	bone

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