Variant report

Variant	rs72620406
Chromosome Location	chr22:32750864-32750865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:32750639-32751129	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr22:32750518-32751254	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr22:32750586-32751198	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr22:32750678-32751221	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr22:32750719-32751115	HUVEC	blood vessel:	n/a	n/a
6	FOXP2	chr22:32750406-32750986	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr22:32750579-32751254	HUVEC	blood vessel:	n/a	n/a
8	TAF1	chr22:32750851-32751086	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr22:32750699-32751118	PFSK-1	brain:	n/a	n/a
10	MYC	chr22:32750770-32750944	HUVEC	blood vessel:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:32750845-32750895	BJ	skin:	n/a
2	chr22:32750845-32750895	BE2_C	brain:	n/a
3	chr22:32750845-32750895	HAEpiC	amniotic membrane:	n/a
4	chr22:32750845-32750895	HIPEpiC	eye:	n/a
5	chr22:32750845-32750895	K562	blood:	n/a
6	chr22:32750845-32750895	HEEpiC	esophagus:	n/a
7	chr22:32750845-32750895	AG10803	skin:	n/a
8	chr22:32750845-32750895	NHDF-neo	bronchial:	n/a
9	chr22:32750845-32750895	HUVEC	blood vessel:	n/a
10	chr22:32750845-32750895	NB4	blood:	n/a
11	chr22:32750845-32750895	HNPCEpiC	eye:	n/a
12	chr22:32750845-32750895	ECC-1	luminal epithelium:	n/a
13	chr22:32750845-32750895	Caco-2	colon:	n/a
14	chr22:32750845-32750895	ovcar-3	ovarian:	n/a
15	chr22:32750845-32750895	HL-60	blood:	n/a
16	chr22:32750845-32750895	GM19239	blood:	n/a
17	chr22:32750845-32750895	Jurkat	blood:	n/a
18	chr22:32750845-32750895	PFSK-1	brain:	n/a
19	chr22:32750845-32750895	GM12892	blood:	n/a
20	chr22:32750845-32750895	HEK293	kidney:	embryo
21	chr22:32750845-32750895	HCT-116	colon:	n/a
22	chr22:32750845-32750895	MCF-7	breast:	n/a
23	chr22:32750845-32750895	PrEC	prostate:	n/a
24	chr22:32750845-32750895	SKMC	muscle:	n/a
25	chr22:32750845-32750895	HRPEpiC	eye:	n/a
26	chr22:32750845-32750895	GM06990	blood:	n/a
27	chr22:32750845-32750895	MCF10A-Er-Src	breast:	n/a
28	chr22:32750845-32750895	AG09309	skin:	n/a
29	chr22:32750845-32750895	ProgFib	skin:	n/a
30	chr22:32750845-32750895	Hela-S3	cervix:	n/a
31	chr22:32750845-32750895	AG04449	skin:	fetal
32	chr22:32750845-32750895	U87	brain:	n/a
33	chr22:32750845-32750895	SAEC	small airway:	n/a
34	chr22:32750845-32750895	NT2-D1	testis:	n/a
35	chr22:32750845-32750895	HMEC	breast:	n/a
36	chr22:32750845-32750895	HRCEpiC	kidney:	n/a
37	chr22:32750845-32750895	A549	lung:	n/a
38	chr22:32750845-32750895	HepG2	liver:	n/a
39	chr22:32750845-32750895	PANC-1	pancreas:	n/a
40	chr22:32750845-32750895	T-47D	breast:	n/a
41	chr22:32750845-32750895	LNCaP	prostate:	n/a
42	chr22:32750845-32750895	SK-N-MC	brain:	n/a
43	chr22:32750845-32750895	RPTEC	kidney:	n/a
44	chr22:32750845-32750895	NH-A	brain:	n/a
45	chr22:32750845-32750895	H1-hESC	embryonic stem cell:	embryo
46	chr22:32750845-32750895	HRE	kidney:	n/a
47	chr22:32750845-32750895	HCM	heart:	n/a
48	chr22:32750845-32750895	HCF	heart:	n/a
49	chr22:32750845-32750895	CMK	blood:	n/a
50	chr22:32750845-32750895	HPAEpiC	pulmonary alveolar:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32360288-32405313..22:32740683-32750950	K562	blood:
2	22:32665993-32670527..22:32740683-32750950	H1-hESC	embryonic stem cell:	embryo
3	22:32513817-32522138..22:32740683-32750950	K562	blood:
4	22:32740683-32750950..22:32846948-32860159	K562	blood:
5	22:32529813-32538538..22:32740683-32750950	H1-hESC	embryonic stem cell:	embryo
6	22:31936958-31958600..22:32740683-32750950	Hela-S3	cervix:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFPL3-AS1-4	chr22:32750834-32751034	NONHSAT084957

No data

Variant related genes	Relation type
RFPL3	TF binding region
RFPL3	CpG island
ENSG00000239674	Chromatin interaction
ENSG00000230866	Chromatin interaction
ENSG00000234479	Chromatin interaction
ENSG00000240647	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000224050	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000214093	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs11089557	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11089560	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635	0.94[AMR][1000 genomes]
rs11912799	0.82[EUR][1000 genomes]
rs12160141	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12160986	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs136471	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16987625	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16990258	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16990262	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16990269	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16990428	0.97[AMR][1000 genomes]
rs16990430	0.97[AMR][1000 genomes]
rs1810450	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2014356	0.85[AMR][1000 genomes]
rs2076041	0.97[AMR][1000 genomes]
rs2076045	0.97[AMR][1000 genomes]
rs2281034	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2281035	0.97[AMR][1000 genomes]
rs2413110	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413111	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28404482	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899184	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35207231	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45593940	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577392	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55844652	0.81[ASN][1000 genomes]
rs5749408	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749409	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749410	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749411	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749412	0.90[ASN][1000 genomes]
rs5749413	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749414	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749427	0.91[AMR][1000 genomes]
rs5749429	0.91[AMR][1000 genomes]
rs5753988	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5754000	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754001	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754003	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5754005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5754006	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754007	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754008	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754009	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754010	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754011	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754012	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754016	0.91[ASN][1000 genomes]
rs5754017	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754018	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754019	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754021	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5754023	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754024	0.89[ASN][1000 genomes]
rs5754025	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754027	0.91[ASN][1000 genomes]
rs5754029	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754030	0.91[ASN][1000 genomes]
rs5754031	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5754032	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754033	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754035	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754036	0.90[ASN][1000 genomes]
rs5754037	0.90[ASN][1000 genomes]
rs5754039	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754040	0.90[ASN][1000 genomes]
rs5754041	0.90[ASN][1000 genomes]
rs5754042	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754044	0.90[ASN][1000 genomes]
rs5754045	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754046	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5754047	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5754048	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754050	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5754065	0.97[AMR][1000 genomes]
rs57606003	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58028985	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58500302	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58637580	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59895149	0.97[AMR][1000 genomes]
rs5998434	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5998451	0.91[ASN][1000 genomes]
rs5998453	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5998457	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5998459	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713790	0.97[AMR][1000 genomes]
rs72617300	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72617301	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72617302	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72620403	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72620404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72620405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72620407	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72620408	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7291329	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7291359	0.95[ASN][1000 genomes]
rs7292163	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs738267	0.91[ASN][1000 genomes]
rs742096	0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs72620406	SLC5A4	cis	Esophagus Muscularis	GTEx
rs72620406	SLC5A4	cis	Adipose Subcutaneous	GTEx
rs72620406	SLC5A4	cis	Muscle Skeletal	GTEx

Chromatin state (count:20 , 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	chr22:32746400-32751000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:32748400-32751000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:32748800-32752000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr22:32749400-32751800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr22:32750000-32751000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
7	chr22:32750200-32751000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr22:32750200-32751000	Active TSS	Adipose Nuclei	Adipose
9	chr22:32750200-32751000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr22:32750200-32751000	Active TSS	Esophagus	oesophagus
11	chr22:32750200-32751000	Active TSS	Left Ventricle	heart
12	chr22:32750200-32751000	Active TSS	Lung	lung
13	chr22:32750200-32751000	Active TSS	Right Atrium	heart
14	chr22:32750400-32751000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr22:32750400-32751000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr22:32750400-32751000	Active TSS	Fetal Muscle Trunk	muscle
17	chr22:32750400-32751000	Flanking Active TSS	HUVEC	blood vessel
18	chr22:32750600-32751000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr22:32750800-32751000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr22:32750800-32755600	Weak transcription	Ovary	ovary

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