Variant report

Variant	rs1977444
Chromosome Location	chr9:18954766-18954767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1006120	0.87[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs10738524	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10757004	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs10757007	1.00[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10757008	1.00[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10757009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10757010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10757011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs10757012	0.86[ASN][1000 genomes]
rs10757016	0.91[CHB][hapmap]
rs10757018	0.85[CHB][hapmap]
rs10757020	0.81[CHB][hapmap]
rs10757022	0.81[CHD][hapmap]
rs10811069	0.86[ASN][1000 genomes]
rs10811072	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10811080	0.83[CHD][hapmap]
rs10811085	0.82[CHB][hapmap]
rs10811092	0.82[CHB][hapmap]
rs10811099	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs10963863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963869	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10963896	0.87[CHB][hapmap]
rs10963898	0.83[CHD][hapmap]
rs10963907	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs10963910	0.82[CHB][hapmap]
rs10963911	0.82[CHB][hapmap]
rs10963912	0.81[CHB][hapmap]
rs11790123	0.81[CHD][hapmap]
rs12553946	0.86[CHB][hapmap]
rs12686643	0.81[ASN][1000 genomes]
rs1327502	0.85[ASN][1000 genomes]
rs17236081	0.86[CHB][hapmap]
rs1854157	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1887444	1.00[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1887445	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1887447	1.00[CEU][hapmap]
rs1932448	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs1932452	0.86[CHB][hapmap]
rs1932453	0.86[CHB][hapmap]
rs2039008	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs2039010	0.87[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs2039011	0.83[CHB][hapmap]
rs2152464	0.81[CHD][hapmap]
rs36098671	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3892045	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4395970	0.91[CHB][hapmap]
rs4419893	0.84[CHD][hapmap]
rs4977269	0.84[ASN][1000 genomes]
rs4977270	0.84[ASN][1000 genomes]
rs4977273	0.83[CHD][hapmap]
rs4977476	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4977477	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977478	0.84[ASN][1000 genomes]
rs4977479	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6475272	0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs6475273	0.82[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs6475274	0.83[ASN][1000 genomes]
rs6475275	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs6475276	0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs6475277	0.84[ASN][1000 genomes]
rs6475279	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs6475283	0.85[CEU][hapmap]
rs6475292	0.87[ASN][1000 genomes]
rs6475293	0.80[ASN][1000 genomes]
rs6475294	0.88[CHD][hapmap]
rs6475295	0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6475296	0.91[CHD][hapmap]
rs7021572	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7024697	0.82[CHB][hapmap]
rs7025123	0.80[JPT][hapmap]
rs7025581	0.83[ASN][1000 genomes]
rs7028858	0.82[CHB][hapmap]
rs7028936	0.82[CHB][hapmap]
rs7034201	0.80[ASN][1000 genomes]
rs7037837	0.82[CHB][hapmap]
rs7038730	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs7044758	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7044864	0.86[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7045059	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7045203	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs7048198	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7848918	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs7849807	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7852907	0.81[CHB][hapmap]
rs7856117	0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7856285	0.91[CEU][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes]
rs7857590	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs7862694	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs7864376	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs7865237	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7865461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7871205	0.81[CHB][hapmap]
rs7871450	0.87[ASN][1000 genomes]
rs7871456	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs883439	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs953734	0.81[CHD][hapmap]

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	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv466282	chr9:18920357-18960393	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv471289	chr9:18920357-18960393	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv613727	chr9:18920357-18960393	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv892699	chr9:18945868-19025693	Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1022697	chr9:18951530-19010894	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1977444	PLIN2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18948200-18955000	Weak transcription	Fetal Thymus	thymus

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