Variant report

Variant	rs57942848
Chromosome Location	chr16:46883118-46883119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1009391	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860484	1.00[ASN][1000 genomes]
rs11861896	1.00[ASN][1000 genomes]
rs11862073	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12934580	1.00[ASN][1000 genomes]
rs1641121	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1641122	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1651654	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16948661	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17189741	0.85[EUR][1000 genomes]
rs1869006	1.00[ASN][1000 genomes]
rs2192644	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341041	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2341043	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36481	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs415018	0.84[EUR][1000 genomes]
rs42461	0.81[EUR][1000 genomes]
rs4246381	1.00[ASN][1000 genomes]
rs4966706	1.00[ASN][1000 genomes]
rs4966708	1.00[ASN][1000 genomes]
rs4966710	1.00[ASN][1000 genomes]
rs4966713	1.00[ASN][1000 genomes]
rs4967576	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	1.00[ASN][1000 genomes]
rs4967621	1.00[ASN][1000 genomes]
rs56042735	1.00[ASN][1000 genomes]
rs57127559	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62057633	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598777	1.00[ASN][1000 genomes]
rs66804065	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67205347	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67211229	1.00[ASN][1000 genomes]
rs67369452	1.00[ASN][1000 genomes]
rs68162608	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs698418	0.83[EUR][1000 genomes]
rs7187475	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7196375	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7197485	1.00[ASN][1000 genomes]
rs7198951	0.85[EUR][1000 genomes]
rs72812428	1.00[ASN][1000 genomes]
rs8044443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045353	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8051017	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8053137	1.00[ASN][1000 genomes]
rs8053297	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058734	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808432	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808434	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs808780	0.81[EUR][1000 genomes]
rs808783	0.85[EUR][1000 genomes]
rs9328668	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889198	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic 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	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1061651	chr16:46721805-46915511	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv1067283	chr16:46801709-46885218	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv3519767	chr16:46873184-46960035	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv3519768	chr16:46873184-46960035	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	esv1795793	chr16:46882046-46904119	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57942848	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46878400-46883200	Weak transcription	Spleen	Spleen
2	chr16:46881600-46883400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr16:46882000-46884200	Weak transcription	HepG2	liver
4	chr16:46882800-46888200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr16:46883000-46883200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr16:46883000-46883400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr16:46883000-46883400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr16:46883000-46883800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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