Variant report

Variant	rs3960769
Chromosome Location	chr4:106451799-106451800
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1352707	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388040	0.96[ASN][1000 genomes]
rs1490599	0.96[ASN][1000 genomes]
rs1490600	0.96[ASN][1000 genomes]
rs1490601	0.96[ASN][1000 genomes]
rs1490602	0.96[ASN][1000 genomes]
rs17035753	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17584200	0.98[ASN][1000 genomes]
rs17839078	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2189228	0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs2866798	0.96[ASN][1000 genomes]
rs2866799	0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs3796916	0.81[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs3796917	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822274	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3974414	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4699186	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4699187	0.96[ASN][1000 genomes]
rs4699188	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6533204	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6533205	0.96[ASN][1000 genomes]
rs6817760	0.96[ASN][1000 genomes]
rs6853877	0.96[ASN][1000 genomes]
rs7666509	0.85[ASN][1000 genomes]
rs7672413	0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.92[ASN][1000 genomes]
rs7686705	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.98[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	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3960769	TET2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106448600-106466200	Weak transcription	Pancreas	Pancrea
2	chr4:106448800-106458000	Weak transcription	Gastric	stomach

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