Variant report

Variant	rs1228939
Chromosome Location	chr7:84122457-84122458
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	chr7:84121738-84122935	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr7:84120723-84122890	SK-N-SH	brain:	n/a	chr7:84122010-84122017
3	GATA2	chr7:84121797-84122693	SH-SY5Y	brain:	n/a	n/a
4	TCF12	chr7:84121384-84122606	ECC-1	luminal epithelium:	n/a	chr7:84122010-84122017
5	TCF12	chr7:84121693-84122596	SK-N-SH	brain:	n/a	chr7:84122010-84122017
6	GATA3	chr7:84121678-84122972	SK-N-SH	brain:	n/a	n/a
7	EP300	chr7:84122391-84122741	SK-N-SH_RA	brain:	n/a	n/a
8	EP300	chr7:84122414-84122794	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
SEMA3A	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1029541	0.96[EUR][1000 genomes]
rs1228859	0.89[CEU][hapmap]
rs1228860	0.90[CEU][hapmap]
rs1228898	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1228909	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1228912	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1228913	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228915	0.97[EUR][1000 genomes]
rs1228916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228919	0.99[EUR][1000 genomes]
rs1228933	0.96[EUR][1000 genomes]
rs1228937	0.97[EUR][1000 genomes]
rs1228938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228943	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1228944	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1228945	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1228947	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1228948	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1228949	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1228950	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1228952	0.80[EUR][1000 genomes]
rs1228953	0.80[EUR][1000 genomes]
rs1228954	0.80[EUR][1000 genomes]
rs1228958	0.80[EUR][1000 genomes]
rs1228959	0.80[EUR][1000 genomes]
rs1228961	0.80[EUR][1000 genomes]
rs1228965	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1228966	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1234538	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1235295	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13223991	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1634614	0.80[EUR][1000 genomes]
rs1715510	0.80[EUR][1000 genomes]
rs2079352	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2527528	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2706902	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2706907	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3094908	0.97[EUR][1000 genomes]
rs505758	0.85[CEU][hapmap]
rs757747	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv2754468	chr7:83851249-84166749	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv534431	chr7:84001059-84138511	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv949446	chr7:84003501-84763823	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv888634	chr7:84086502-84196258	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv888635	chr7:84086502-84344258	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv888636	chr7:84117594-84334498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:84114000-84130600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:84122000-84122600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:84122000-84125400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:84122200-84122600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:84122200-84122800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:84122200-84122800	Enhancers	Adipose Nuclei	Adipose
7	chr7:84122200-84122800	Enhancers	NHDF-Ad	bronchial
8	chr7:84122400-84123000	Enhancers	Pancreatic Islets	Pancreatic Islet

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