Variant report

Variant	rs338979
Chromosome Location	chr3:120950098-120950099
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1191288	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1191290	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1191293	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1191296	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1191297	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1191300	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1191309	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1211513	0.86[EUR][1000 genomes]
rs12487633	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13434156	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1397824	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1511432	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588538	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1688683	0.85[EUR][1000 genomes]
rs17195196	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs173087	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795387	0.90[EUR][1000 genomes]
rs1795390	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1795392	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1795404	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2141658	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331521	0.85[EUR][1000 genomes]
rs2331527	0.87[EUR][1000 genomes]
rs2331709	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234997	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2656043	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656048	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701057	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338958	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338959	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338969	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs338973	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs338981	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338983	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338994	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338996	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339000	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339006	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339011	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34168323	0.93[EUR][1000 genomes]
rs35345840	0.85[EUR][1000 genomes]
rs35645356	0.92[EUR][1000 genomes]
rs3845849	0.87[EUR][1000 genomes]
rs3856575	0.93[EUR][1000 genomes]
rs3914744	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4048751	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4510329	0.87[EUR][1000 genomes]
rs4630876	0.85[EUR][1000 genomes]
rs60648200	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6775508	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6782025	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap]
rs6782033	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap]
rs6784156	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787048	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs6798699	1.00[JPT][hapmap]
rs6805670	0.87[EUR][1000 genomes]
rs6807604	0.86[EUR][1000 genomes]
rs7615712	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7615991	0.89[EUR][1000 genomes]
rs7616466	0.90[EUR][1000 genomes]
rs7632907	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs7635903	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7648360	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9844667	0.87[EUR][1000 genomes]
rs9853078	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9860056	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9866746	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1005275	chr3:120700604-121102735	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1008441	chr3:120730017-121102735	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv536709	chr3:120730017-121102735	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1005525	chr3:120749594-121027161	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1012777	chr3:120883846-120974864	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv829701	chr3:120935402-121115932	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv517501	chr3:120941578-120970900	Enhancers Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
11	nsv518828	chr3:120941578-120977383	Enhancers Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs338979	CHST13	cis	parietal	SCAN
rs338979	STXBP5L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120936400-120955800	Weak transcription	Ovary	ovary
2	chr3:120945400-120965200	Weak transcription	Brain Anterior Caudate	brain
3	chr3:120950000-120950800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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