Variant report

Variant	rs12974758
Chromosome Location	chr19:21667302-21667303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10420016	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11668606	0.82[EUR][1000 genomes]
rs11671579	0.81[EUR][1000 genomes]
rs1879234	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2173727	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2359155	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562398	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2562408	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2562417	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562428	0.80[ASN][1000 genomes]
rs2562456	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562466	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562468	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562471	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562474	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2562487	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2562507	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2562508	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2650773	0.82[ASN][1000 genomes]
rs2650784	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650792	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2650793	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2650801	0.81[ASN][1000 genomes]
rs2650804	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2650805	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2650814	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2650819	0.82[ASN][1000 genomes]
rs2650825	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2681370	0.82[EUR][1000 genomes]
rs2681377	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681388	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2681389	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2681391	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681392	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2681395	0.82[EUR][1000 genomes]
rs2914646	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2946790	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2968076	0.80[ASN][1000 genomes]
rs2968078	0.82[ASN][1000 genomes]
rs35008138	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4524067	0.83[EUR][1000 genomes]
rs58001930	0.82[EUR][1000 genomes]
rs62110163	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6511250	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6511253	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6511254	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6511256	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511258	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7252585	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8106025	0.82[ASN][1000 genomes]
rs9304986	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9304987	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv510759	chr19:21664791-21723191	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12974758	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs12974758	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs12974758	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs12974758	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12974758	CTD-2561J22.5	cis	Thyroid	GTEx
rs12974758	ZNF708	cis	Muscle Skeletal	GTEx
rs12974758	ZNF708	cis	lung	GTEx
rs12974758	RP11-678G14.3	cis	lung	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21658200-21667400	Weak transcription	Right Atrium	heart
2	chr19:21658200-21687800	Weak transcription	Brain Substantia Nigra	brain
3	chr19:21659200-21668400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:21666000-21668600	Weak transcription	Stomach Mucosa	stomach
5	chr19:21666200-21668400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr19:21666200-21668600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:21666200-21669400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:21666400-21668400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:21666800-21668400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:21666800-21668400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:21666800-21668400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:21666800-21670200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:21666800-21687600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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