Variant report

Variant	rs6848028
Chromosome Location	chr4:104279946-104279947
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10005997	1.00[ASN][1000 genomes]
rs10026360	0.93[ASN][1000 genomes]
rs11946500	0.93[ASN][1000 genomes]
rs12499479	0.83[EUR][1000 genomes]
rs12502466	0.88[EUR][1000 genomes]
rs1512275	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17033646	0.94[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs17220904	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs17221044	0.92[ASN][1000 genomes]
rs17286262	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615487	0.93[ASN][1000 genomes]
rs35091078	0.93[ASN][1000 genomes]
rs35478417	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698894	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699069	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699070	0.95[ASN][1000 genomes]
rs4699071	0.92[ASN][1000 genomes]
rs55784701	0.88[EUR][1000 genomes]
rs57215821	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58909279	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59776785	0.88[EUR][1000 genomes]
rs62338903	0.85[EUR][1000 genomes]
rs62338908	0.87[EUR][1000 genomes]
rs62338932	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62338936	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533085	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816172	0.85[EUR][1000 genomes]
rs6822395	0.88[EUR][1000 genomes]
rs6838853	0.85[EUR][1000 genomes]
rs6844296	0.88[EUR][1000 genomes]
rs6844334	0.88[EUR][1000 genomes]
rs6857044	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72935453	0.93[ASN][1000 genomes]
rs7671327	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7675703	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv2757947	chr4:104179925-104342395	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2759271	chr4:104179925-104342395	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3348747	chr4:104214627-104609795	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv879686	chr4:104260725-104335667	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6848028	TET2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104279200-104282200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
2	chr4:104279600-104282600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links