Variant report

Variant	rs1534290
Chromosome Location	chr2:178877602-178877603
allele	A/G
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	chr2:178877584-178877705	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000236664	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10930814	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs12463866	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs12469439	0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1344923	0.80[MEX][hapmap]
rs1369519	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1405643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1405644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1405645	1.00[YRI][hapmap]
rs1405646	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1435575	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs16865995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16866042	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880915	0.96[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2037757	0.96[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2099476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2217839	1.00[YRI][hapmap]
rs2695094	0.89[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2695104	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2695111	0.84[CEU][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2695112	0.92[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2695729	0.96[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2695735	0.85[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap]
rs2695738	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2695744	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs2695747	0.86[JPT][hapmap]
rs2695754	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108453	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs3108476	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs3770051	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs4893847	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62185280	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6433705	0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6743194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6753870	0.82[EUR][1000 genomes]
rs7573622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs934807	0.96[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs959157	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs959792	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1007579	chr2:178729330-178890946	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875451	chr2:178748294-178953409	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv998304	chr2:178756380-178924378	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv536056	chr2:178756380-178924378	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178873600-178882800	Weak transcription	Pancreas	Pancrea
2	chr2:178873600-178889600	Weak transcription	A549	lung

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