Variant report

Variant	rs4680913
Chromosome Location	chr3:28431394-28431395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:28431363-28431510	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ZCWPW2	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11706332	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs11707705	1.00[CHB][hapmap]
rs11709034	0.82[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs11712484	1.00[CHB][hapmap]
rs11712489	1.00[CHB][hapmap]
rs11720107	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs11918050	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs11921692	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs11921943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11924173	0.80[ASN][1000 genomes]
rs12107256	0.85[CHB][hapmap]
rs13065010	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13069839	0.85[ASN][1000 genomes]
rs13070434	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13075840	1.00[CHB][hapmap]
rs13081520	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13082167	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13083544	0.85[CHB][hapmap]
rs13085075	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13087143	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13087774	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13088574	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13090296	0.85[CHB][hapmap]
rs13090439	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs13093242	0.85[CHB][hapmap]
rs13095628	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs13095675	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13101128	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1457910	1.00[CHB][hapmap]
rs1585211	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1598846	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs1599826	0.92[CHB][hapmap]
rs1606386	0.92[CHB][hapmap]
rs1606388	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs1606393	0.89[CEU][hapmap]
rs1610238	0.85[CHB][hapmap]
rs17021221	0.85[CHB][hapmap]
rs17021306	0.85[CHB][hapmap]
rs17021402	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs17357206	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs17638742	0.92[CHB][hapmap]
rs17638991	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs17695765	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs17695884	1.00[CHB][hapmap]
rs17696025	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs17696459	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs17696783	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1870259	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1975828	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1975829	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2018136	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168799	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35088087	0.80[ASN][1000 genomes]
rs36051688	0.80[ASN][1000 genomes]
rs36105900	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs3762797	1.00[CHB][hapmap]
rs4234338	0.84[CHB][hapmap]
rs4327342	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4452283	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs4585155	0.89[CEU][hapmap]
rs4680750	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680909	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680910	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58918848	0.80[ASN][1000 genomes]
rs59975750	0.82[ASN][1000 genomes]
rs6551255	0.80[ASN][1000 genomes]
rs6762636	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6763313	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6771057	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771460	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs6777813	0.81[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs6803692	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68085718	0.80[ASN][1000 genomes]
rs7434193	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7639750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7641491	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7643191	1.00[CHB][hapmap]
rs7649498	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7650742	0.85[EUR][1000 genomes]
rs7651883	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310865	0.92[YRI][hapmap]
rs969443	1.00[CHB][hapmap]
rs9843464	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv876650	chr3:28427029-28613602	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4680913	OSBPL10	cis	parietal	SCAN
rs4680913	RGS19	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28420800-28433000	Weak transcription	Ovary	ovary
2	chr3:28425200-28431400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:28426000-28433000	Weak transcription	Right Ventricle	heart

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