Variant report

Variant	rs28404482
Chromosome Location	chr22:32751376-32751377
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr22:32751016-32751388	GM12878	blood:	n/a	n/a
2	SP1	chr22:32750876-32751435	H1-hESC	embryonic stem cell:	n/a	n/a
3	NFYB	chr22:32750914-32751408	K562	blood:	n/a	chr22:32751119-32751134 chr22:32751175-32751190 chr22:32751151-32751166

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32529813-32538538..22:32750950-32761732	K562	blood:
2	22:32360288-32405313..22:32750950-32761732	K562	blood:
3	22:32665993-32670527..22:32750950-32761732	K562	blood:
4	22:31936958-31958600..22:32750950-32761732	Hela-S3	cervix:
5	22:32513817-32522138..22:32750950-32761732	H1-hESC	embryonic stem cell:	embryo
6	22:32750950-32761732..22:33253287-33262063	Hela-S3	cervix:
7	22:32284948-32287956..22:32750950-32761732	K562	blood:

Variant related genes	Relation type
RFPL3	TF binding region
ENSG00000230866	Chromatin interaction
ENSG00000227813	Chromatin interaction
ENSG00000183531	Chromatin interaction
ENSG00000239674	Chromatin interaction
ENSG00000240647	Chromatin interaction
ENSG00000224050	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000234479	Chromatin interaction
ENSG00000214093	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11089557	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11089560	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11635	0.88[AMR][1000 genomes]
rs12160141	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12160986	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs136471	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16987625	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16990258	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16990262	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16990269	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16990428	0.91[AMR][1000 genomes]
rs16990430	0.91[AMR][1000 genomes]
rs1810450	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076041	0.91[AMR][1000 genomes]
rs2076045	0.91[AMR][1000 genomes]
rs2281034	0.88[AMR][1000 genomes]
rs2281035	0.91[AMR][1000 genomes]
rs2413110	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2413111	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899184	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35207231	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45593940	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577392	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55844652	0.81[ASN][1000 genomes]
rs5749408	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749409	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749410	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749411	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749412	0.90[ASN][1000 genomes]
rs5749413	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749414	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5749427	0.86[AMR][1000 genomes]
rs5749429	0.86[AMR][1000 genomes]
rs5753988	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5754000	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754001	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754003	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5754005	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5754006	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754007	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754008	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754009	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754010	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754011	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754012	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754016	0.91[ASN][1000 genomes]
rs5754017	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754018	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754019	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754021	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5754023	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754024	0.90[ASN][1000 genomes]
rs5754025	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754027	0.91[ASN][1000 genomes]
rs5754029	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754030	0.91[ASN][1000 genomes]
rs5754031	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5754032	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754033	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754035	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754036	0.90[ASN][1000 genomes]
rs5754037	0.90[ASN][1000 genomes]
rs5754039	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754040	0.90[ASN][1000 genomes]
rs5754041	0.90[ASN][1000 genomes]
rs5754042	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754044	0.90[ASN][1000 genomes]
rs5754045	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754046	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5754047	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754048	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754050	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5754065	0.91[AMR][1000 genomes]
rs57606003	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58028985	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58500302	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58637580	0.85[AMR][1000 genomes]
rs59895149	0.91[AMR][1000 genomes]
rs5998434	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5998451	0.91[ASN][1000 genomes]
rs5998453	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5998457	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5998459	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713790	0.91[AMR][1000 genomes]
rs72617300	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72617301	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72617302	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72620403	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72620404	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72620405	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72620406	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72620407	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72620408	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7291329	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7291359	0.95[ASN][1000 genomes]
rs7292163	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs738267	0.91[ASN][1000 genomes]
rs742096	0.91[AMR][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	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
9	nsv964624	chr22:32740318-32751906	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28404482	SLC5A4	cis	Adipose Subcutaneous	GTEx
rs28404482	SLC5A4	cis	Muscle Skeletal	GTEx
rs28404482	SLC5A4	cis	Esophagus Muscularis	GTEx
rs28404482	RFPL3S	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32740200-32752000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:32748800-32752000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr22:32749400-32751800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr22:32750800-32755600	Weak transcription	Ovary	ovary
5	chr22:32751000-32751600	Enhancers	HUVEC	blood vessel
6	chr22:32751000-32752000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr22:32751000-32754200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:32751200-32751400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr22:32751200-32752000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:32751200-32752200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr22:32751200-32752400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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