Variant report

Variant	rs3907818
Chromosome Location	chr6:54278274-54278275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12196685	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12209833	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12215230	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13195267	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13201270	0.86[AMR][1000 genomes]
rs1508631	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1876606	0.87[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2173375	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6919229	0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9349706	0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9367570	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9370291	0.87[ASW][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9395942	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3907818	TFAP2D	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54269400-54284400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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