Variant report

Variant	rs6542846
Chromosome Location	chr2:99563654-99563655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10165534	0.84[EUR][1000 genomes]
rs10167390	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10170063	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10179910	0.82[EUR][1000 genomes]
rs10181422	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10193019	0.81[EUR][1000 genomes]
rs10196680	0.84[EUR][1000 genomes]
rs10202452	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1115756	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1115757	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1133977	0.81[ASN][1000 genomes]
rs1133978	0.80[ASN][1000 genomes]
rs11683107	0.82[ASN][1000 genomes]
rs11683188	0.82[ASN][1000 genomes]
rs11688004	0.82[ASN][1000 genomes]
rs11692336	0.82[ASN][1000 genomes]
rs11895749	0.82[ASN][1000 genomes]
rs11903311	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12464710	0.84[EUR][1000 genomes]
rs12467679	0.83[EUR][1000 genomes]
rs12470471	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12473029	0.90[EUR][1000 genomes]
rs12477754	0.84[EUR][1000 genomes]
rs12477978	0.90[EUR][1000 genomes]
rs12613624	0.82[ASN][1000 genomes]
rs12619780	0.84[ASN][1000 genomes]
rs12987548	0.83[ASN][1000 genomes]
rs13008171	0.82[ASN][1000 genomes]
rs13396358	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13407840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13412764	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1349778	0.83[EUR][1000 genomes]
rs1349779	0.91[EUR][1000 genomes]
rs1453563	0.83[ASN][1000 genomes]
rs1453564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530996	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1563106	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1563107	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1563108	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1580068	0.84[EUR][1000 genomes]
rs17708262	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17759607	0.82[ASN][1000 genomes]
rs2084988	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2309524	0.81[EUR][1000 genomes]
rs2516830	0.82[ASN][1000 genomes]
rs2516833	0.81[ASN][1000 genomes]
rs2516835	0.82[ASN][1000 genomes]
rs2632283	0.82[ASN][1000 genomes]
rs28575117	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28648058	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34272114	0.82[ASN][1000 genomes]
rs35001733	0.82[EUR][1000 genomes]
rs4346438	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4585080	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4622780	0.83[EUR][1000 genomes]
rs4850897	0.82[ASN][1000 genomes]
rs4851179	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4851183	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4851188	0.82[ASN][1000 genomes]
rs62154638	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62156558	0.85[AMR][1000 genomes]
rs6542852	0.85[EUR][1000 genomes]
rs6542858	0.81[EUR][1000 genomes]
rs6542866	0.82[ASN][1000 genomes]
rs6542868	0.82[ASN][1000 genomes]
rs6704766	0.84[EUR][1000 genomes]
rs6707462	0.86[ASN][1000 genomes]
rs6721535	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6722164	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6724476	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6732579	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6735801	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6736064	0.83[EUR][1000 genomes]
rs6737257	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6740035	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6740054	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6740267	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6753650	0.83[ASN][1000 genomes]
rs6754843	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6759354	0.84[EUR][1000 genomes]
rs720229	0.85[ASN][1000 genomes]
rs72957109	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7558239	0.84[EUR][1000 genomes]
rs7570657	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7571390	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586608	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7588059	0.88[ASN][1000 genomes]
rs7591794	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7599427	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7605734	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7606635	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7608938	0.82[ASN][1000 genomes]
rs896886	0.83[EUR][1000 genomes]
rs9308816	0.84[EUR][1000 genomes]
rs9808541	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6542846	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs6542846	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs6542846	TSGA10	cis	multi-tissue	Pritchard
rs6542846	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6542846	TSGA10	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99557000-99565200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:99561600-99564400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:99562200-99565400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:99563000-99566200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:99563400-99563800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:99563400-99563800	Enhancers	Fetal Brain Male	brain
7	chr2:99563400-99563800	Enhancers	Ovary	ovary
8	chr2:99563600-99563800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:99563600-99564600	Enhancers	Fetal Brain Female	brain
10	chr2:99563600-99566000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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