Variant report

Variant	rs3829658
Chromosome Location	chr19:52000672-52000673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52000624..52003424-chr19:52007284..52010665,4	K562	blood:

Variant related genes	Relation type
ENSG00000268839	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10404542	0.82[JPT][hapmap]
rs10420446	0.87[EUR][1000 genomes]
rs10420457	0.92[CEU][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs1160392	0.82[EUR][1000 genomes]
rs1551556	0.82[ASW][hapmap];0.84[CEU][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs16982743	0.81[MEX][hapmap];0.80[YRI][hapmap]
rs2009362	0.82[ASW][hapmap];0.92[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2168643	0.81[TSI][hapmap]
rs2864101	0.82[EUR][1000 genomes]
rs2864102	0.81[EUR][1000 genomes]
rs2864103	0.81[EUR][1000 genomes]
rs2864104	0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs3810106	0.85[EUR][1000 genomes]
rs3810108	0.87[EUR][1000 genomes]
rs3810110	0.82[ASW][hapmap];0.92[CEU][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs3810114	0.82[JPT][hapmap]
rs3826667	0.90[ASN][1000 genomes]
rs3976745	0.80[EUR][1000 genomes]
rs4801873	0.82[EUR][1000 genomes]
rs4801874	0.81[TSI][hapmap]
rs6509544	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs7253637	0.80[CHD][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs7255948	0.81[CEU][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs8102707	0.82[ASW][hapmap];0.84[CEU][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs9304718	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs968491	0.91[CHB][hapmap];0.94[JPT][hapmap]

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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3829658	SIGLEC12	cis	Nerve Tibial	GTEx
rs3829658	SIGLEC12	cis	lung	GTEx
rs3829658	SIGLEC12	cis	Artery Aorta	GTEx
rs3829658	SIGLEC12	cis	Skin Sun Exposed Lower leg	GTEx
rs3829658	SIGLEC12	cis	Artery Tibial	GTEx
rs3829658	RDH13	cis	parietal	SCAN
rs3829658	SIGLEC12	cis	Adipose Subcutaneous	GTEx
rs3829658	ZNF468	cis	cerebellum	SCAN
rs3829658	ZNF584	cis	parietal	SCAN
rs3829658	SIGLEC12	cis	Thyroid	GTEx
rs3829658	SIGLEC12	cis	Esophagus Mucosa	GTEx
rs3829658	CXXC4	trans	cerebellum	SCAN
rs3829658	SIGLEC12	cis	Whole Blood	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51996400-52002600	Weak transcription	Spleen	Spleen
2	chr19:51997800-52002600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr19:51997800-52002800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr19:52000000-52002800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:52000600-52001800	Enhancers	K562	blood

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