Variant report

Variant	rs16987839
Chromosome Location	chr22:29983138-29983139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1006396	0.87[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs1049534	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs11704899	0.83[TSI][hapmap]
rs11705569	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16987832	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2009354	0.92[YRI][hapmap]
rs2074948	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs2074951	0.92[YRI][hapmap]
rs2188120	0.92[YRI][hapmap]
rs2247753	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2262240	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302141	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs2530656	0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2530658	0.87[ASN][1000 genomes]
rs2530664	0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs2531848	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs425992	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs433194	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs456285	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs456585	0.86[ASN][1000 genomes]
rs458196	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs459450	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs460428	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.81[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs460994	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs462444	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs463220	0.89[ASN][1000 genomes]
rs468224	0.82[EUR][1000 genomes]
rs468254	0.86[ASN][1000 genomes]
rs468475	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs468852	0.86[ASN][1000 genomes]
rs469230	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs469253	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs469295	0.91[ASN][1000 genomes]
rs469363	0.83[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs469565	0.82[ASN][1000 genomes]
rs5763297	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs5763301	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs5763303	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs5763305	0.87[JPT][hapmap];0.93[TSI][hapmap]
rs5763306	0.91[JPT][hapmap];0.92[YRI][hapmap]
rs5763349	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs695525	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs695668	0.83[AFR][1000 genomes]
rs695780	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs695816	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73159040	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7609	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs8135828	0.87[JPT][hapmap];0.93[TSI][hapmap]
rs8141518	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv521852	chr22:29974831-29983138	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs16987839	THOC5	cis	Muscle Skeletal	GTEx
rs16987839	THOC5	cis	Artery Tibial	GTEx
rs16987839	THOC5	cis	Thyroid	GTEx
rs16987839	THOC5	cis	Adipose Subcutaneous	GTEx
rs16987839	NIPSNAP1	cis	Stomach	GTEx
rs16987839	THOC5	cis	Artery Aorta	GTEx
rs16987839	THOC5	cis	Esophagus Muscularis	GTEx
rs16987839	THOC5	cis	Nerve Tibial	GTEx
rs16987839	THOC5	cis	lung	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29977600-29998800	Weak transcription	Right Atrium	heart
2	chr22:29977800-29984000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr22:29977800-29994200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:29978000-29983200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr22:29978200-29983600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr22:29978200-29983600	Weak transcription	HMEC	breast
7	chr22:29978200-29984000	Weak transcription	Hela-S3	cervix
8	chr22:29978400-29983200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr22:29979000-29990000	Weak transcription	K562	blood
10	chr22:29981400-29983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr22:29981600-29983800	Weak transcription	HepG2	liver

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