Variant report

Variant	rs9296268
Chromosome Location	chr6:38899485-38899486
allele	C/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	chr6:38899335-38899499	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000231150	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1018437	1.00[CHB][hapmap]
rs1678638	0.90[CHB][hapmap]
rs1678717	0.90[CHB][hapmap]
rs1678742	1.00[CHB][hapmap]
rs1738184	0.90[CHB][hapmap]
rs1738203	0.89[CHB][hapmap]
rs1929900	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2179564	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2395709	1.00[CHB][hapmap]
rs3734612	0.91[CEU][hapmap];0.89[TSI][hapmap]
rs4286777	1.00[CHB][hapmap]
rs4380739	1.00[CHB][hapmap]
rs4386804	1.00[CHB][hapmap]
rs4391252	1.00[CHB][hapmap]
rs4443498	1.00[CHB][hapmap]
rs4571559	1.00[CHB][hapmap]
rs4590258	1.00[CHB][hapmap]
rs4711558	1.00[CHB][hapmap]
rs4714193	1.00[CHB][hapmap]
rs4714200	0.91[CEU][hapmap]
rs6458080	1.00[CHB][hapmap]
rs6458081	1.00[CHB][hapmap]
rs6458087	0.91[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6905467	0.91[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6928176	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6931736	1.00[CHB][hapmap]
rs6933584	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6933965	0.91[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6940724	0.91[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs7357080	0.87[CHD][hapmap];0.93[GIH][hapmap]
rs7752004	0.93[GIH][hapmap]
rs862422	0.90[CHB][hapmap]
rs862425	0.90[CHB][hapmap]
rs862438	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs862439	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9296265	1.00[CHB][hapmap]
rs9357290	1.00[CHB][hapmap]
rs9366982	1.00[CHB][hapmap]
rs9369089	1.00[CHB][hapmap]
rs9369091	0.90[CHD][hapmap]
rs9380789	1.00[CHB][hapmap]
rs9380791	1.00[CHB][hapmap]
rs9380796	1.00[CHB][hapmap]
rs9380798	1.00[CHB][hapmap]
rs9380799	1.00[CHB][hapmap]
rs9394547	1.00[CHB][hapmap]
rs9394550	1.00[CHB][hapmap]

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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462918	chr6:38875752-38901236	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv602961	chr6:38875752-38901236	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9296268	LRFN2	cis	cerebellum	SCAN
rs9296268	TMEM129	trans	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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