Variant report

Variant	rs5753988
Chromosome Location	chr22:32737548-32737549
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11089557	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11089560	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11635	0.91[AMR][1000 genomes]
rs12160141	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12160986	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs136471	0.91[AMR][1000 genomes]
rs16987625	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16990258	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16990262	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16990269	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16990428	0.88[AMR][1000 genomes]
rs16990430	0.88[AMR][1000 genomes]
rs1810450	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2076041	0.88[AMR][1000 genomes]
rs2076045	0.88[AMR][1000 genomes]
rs2281034	0.91[AMR][1000 genomes]
rs2281035	0.88[AMR][1000 genomes]
rs2413110	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2413111	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28404482	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2899184	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35207231	0.88[EUR][1000 genomes]
rs45593940	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4577392	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5749408	0.91[EUR][1000 genomes]
rs5749409	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5749410	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5749411	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5749413	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5749414	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5749427	0.83[AMR][1000 genomes]
rs5749429	0.83[AMR][1000 genomes]
rs5753989	0.96[ASN][1000 genomes]
rs5753990	0.93[ASN][1000 genomes]
rs5753991	0.94[ASN][1000 genomes]
rs5754000	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5754001	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5754003	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5754005	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5754006	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754007	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754008	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754009	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5754010	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754011	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754012	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754017	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754018	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754019	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754021	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5754023	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754025	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754029	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754031	0.85[EUR][1000 genomes]
rs5754032	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754033	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754035	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754039	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754042	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754045	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754046	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754047	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754048	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754050	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754065	0.88[AMR][1000 genomes]
rs57606003	0.81[EUR][1000 genomes]
rs58028985	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58500302	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59895149	0.88[AMR][1000 genomes]
rs5998434	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5998453	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5998457	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5998459	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs713790	0.88[AMR][1000 genomes]
rs72617300	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72617301	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72617302	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72620403	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72620404	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72620405	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72620406	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72620407	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72620408	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7285471	0.93[ASN][1000 genomes]
rs7292163	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs742096	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948789	chr22:32462505-32764760	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1065175	chr22:32467617-32761093	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv544680	chr22:32467617-32761093	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv2830423	chr22:32477718-32767825	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv2422247	chr22:32486448-32788258	Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5753988	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32732200-32737600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr22:32735400-32739600	Weak transcription	HUVEC	blood vessel
3	chr22:32736000-32737800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:32736400-32741800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr22:32736600-32737600	Active TSS	Spleen	Spleen
6	chr22:32736800-32737600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
7	chr22:32736800-32744200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:32737000-32737800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:32737000-32737800	Flanking Active TSS	Brain Substantia Nigra	brain
10	chr22:32737400-32737600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr22:32737400-32737600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:32737400-32738000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:32737400-32740000	Weak transcription	Right Atrium	heart

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