Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:173720263-173720390	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
RAPGEF4	TF binding region

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11900684	0.83[CEU][hapmap]
rs16860895	0.86[CEU][hapmap]
rs16860911	0.86[CEU][hapmap]
rs16860920	0.86[CEU][hapmap]
rs16860958	0.86[CEU][hapmap]
rs16860971	0.84[CEU][hapmap]
rs16860975	0.86[CEU][hapmap]
rs16860984	0.86[CEU][hapmap]
rs2194715	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs2194717	0.86[CEU][hapmap]
rs2258081	0.86[CEU][hapmap]
rs34469004	0.93[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs3754762	0.87[CHD][hapmap]
rs3754764	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769274	0.86[ASN][1000 genomes]
rs3769286	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769292	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769293	0.84[EUR][1000 genomes]
rs3769294	0.89[ASN][1000 genomes]
rs3769298	0.84[ASN][1000 genomes]
rs3769302	1.00[CHB][hapmap]
rs59080171	0.84[ASN][1000 genomes]
rs724997	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs72906197	0.84[EUR][1000 genomes]
rs72908203	0.84[EUR][1000 genomes]
rs73977711	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs956752	SHARPIN	cis	Frontal Cortex	GTEx
rs956752	GPIHBP1	cis	Frontal Cortex	GTEx
rs956752	NME3	cis	Frontal Cortex	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173689200-173723200	Weak transcription	Esophagus	oesophagus
2	chr2:173714800-173722200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:173717600-173722400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:173719800-173724400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:173720000-173723000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:173720000-173723200	Weak transcription	Brain Anterior Caudate	brain

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