Variant report

Variant	rs62287394
Chromosome Location	chr4:8474949-8474950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:8474920-8475070	HVMF	connective:	n/a	n/a
2	HMGN3	chr4:8474946-8475199	K562	blood:	n/a	n/a
3	MAZ	chr4:8473745-8475523	IMR90	lung:	n/a	n/a
4	RAD21	chr4:8474911-8475026	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAFK	chr4:8474524-8475027	IMR90	lung:	n/a	chr4:8474666-8474680
6	CTCF	chr4:8474920-8475070	HMF	breast:	n/a	n/a
7	CTCF	chr4:8474633-8475203	IMR90	lung:	n/a	n/a
8	CTCF	chr4:8474900-8475050	HCFaa	heart:	n/a	n/a
9	CTCF	chr4:8474900-8475050	WI-38	lung:	n/a	n/a
10	POLR2A	chr4:8474550-8474972	U87	brain:	n/a	n/a
11	CTCF	chr4:8474860-8475010	HPF	lung:	n/a	n/a
12	CTCF	chr4:8474940-8475090	AG09309	skin:	n/a	n/a
13	CTCF	chr4:8474895-8475050	Kidney_OC	kidney:	n/a	n/a
14	CTCF	chr4:8474900-8475050	HCM	heart:	n/a	n/a
15	CTCF	chr4:8474900-8475050	AG09319	gingival:	n/a	n/a
16	CTCF	chr4:8474840-8474990	HA-sp	spinal cord:	n/a	n/a
17	CTCF	chr4:8474920-8475070	HCPEpiC	choroid plexus:	n/a	n/a
18	CTCF	chr4:8474880-8475030	BJ	skin:	n/a	n/a
19	CTCF	chr4:8474920-8475070	AG04449	skin:	n/a	n/a
20	CTCF	chr4:8474940-8475090	AoAF	blood vessel:	n/a	n/a
21	RCOR1	chr4:8473748-8475315	IMR90	lung:	n/a	n/a
22	CTCF	chr4:8474920-8475070	AG09319	gingival:	n/a	n/a
23	CTCF	chr4:8474900-8475050	AoAF	blood vessel:	n/a	n/a
24	CTCF	chr4:8474820-8474970	AG04449	skin:	n/a	n/a
25	POLR2A	chr4:8474932-8475132	Hela-S3	cervix:	n/a	n/a
26	ESR1	chr4:8474682-8475103	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr4:8474717-8475425	GM12878	blood:	n/a	n/a
28	CTCF	chr4:8474900-8475050	HA-sp	spinal cord:	n/a	n/a
29	CTCF	chr4:8474820-8474970	NHLF	lung:	n/a	n/a
30	RAD21	chr4:8474504-8475220	IMR90	lung:	n/a	n/a
31	TCF7L2	chr4:8474648-8474996	PANC-1	pancreas:	n/a	n/a
32	CTCF	chr4:8474820-8474970	AG04450	lung:	n/a	n/a
33	POLR2A	chr4:8470406-8476371	K562	blood:	n/a	n/a
34	CTCF	chr4:8474940-8475090	HPF	lung:	n/a	n/a
35	CTCF	chr4:8474905-8475113	Gliobla	brain:	n/a	n/a
36	CEBPB	chr4:8474442-8475366	IMR90	lung:	n/a	n/a
37	CTCF	chr4:8474860-8475010	HRE	kidney:	n/a	n/a
38	MXI1	chr4:8473812-8475319	IMR90	lung:	n/a	n/a
39	CTCF	chr4:8474880-8475030	HBMEC	blood vessel:	n/a	n/a
40	CTCF	chr4:8474800-8474950	HFF	foreskin:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8472049..8473735-chr4:8474244..8476711,2	K562	blood:
2	chr4:8471024..8473735-chr4:8474244..8476611,2	K562	blood:

No data

Variant related genes	Relation type
TRMT44	TF binding region
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1060617	0.87[EUR][1000 genomes]
rs1106591	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13434465	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16842352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17194220	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17201848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17202499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17203215	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17203243	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17806817	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17806883	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17807929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17807994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28507650	0.87[EUR][1000 genomes]
rs28664136	0.87[EUR][1000 genomes]
rs61739067	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62286002	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286003	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286005	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286035	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286036	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286037	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286038	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286040	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286041	0.87[EUR][1000 genomes]
rs62286042	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286043	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286044	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62286047	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286049	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286050	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286052	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286053	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286054	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286055	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286056	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62286058	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62286059	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62287360	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62287361	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62287362	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62287382	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62287383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62287384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62287385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62287387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62287390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62287391	0.84[EUR][1000 genomes]
rs62287392	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62287393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62287395	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62287396	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62287397	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62287399	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62287401	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62287402	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62287405	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62287406	0.93[EUR][1000 genomes]
rs62287433	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62287434	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62287435	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62287436	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62287439	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62287440	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62287441	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7686109	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs940132	1.00[AMR][1000 genomes];0.93[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	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8447000-8475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
5	chr4:8459800-8478800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:8463800-8478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:8465200-8482200	Strong transcription	Brain Germinal Matrix	brain
8	chr4:8465400-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:8467600-8475800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:8467600-8482200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:8467800-8480400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:8468000-8478600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:8468400-8479600	Weak transcription	Psoas Muscle	Psoas
14	chr4:8470000-8475400	Weak transcription	Small Intestine	intestine
15	chr4:8470600-8479000	Weak transcription	Fetal Brain Male	brain
16	chr4:8471200-8475200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:8471200-8475200	Enhancers	Ovary	ovary
18	chr4:8471200-8476800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:8471200-8477400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:8471200-8480600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr4:8471400-8477200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:8471400-8477400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:8471400-8477400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:8471400-8479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:8471400-8480200	Weak transcription	HMEC	breast
26	chr4:8471600-8477200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:8471600-8477800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr4:8471800-8477200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:8471800-8477600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr4:8471800-8477600	Weak transcription	A549	lung
31	chr4:8471800-8479600	Weak transcription	NHEK	skin
32	chr4:8471800-8480000	Weak transcription	GM12878-XiMat	blood
33	chr4:8471800-8480800	Weak transcription	HepG2	liver
34	chr4:8471800-8483200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:8472000-8477000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:8472000-8480200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr4:8472200-8475600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:8472200-8477400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:8472200-8480800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:8472400-8477400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:8472400-8479800	Weak transcription	Primary B cells from cord blood	blood
42	chr4:8472600-8480000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr4:8472800-8475000	Weak transcription	Aorta	Aorta
44	chr4:8472800-8475400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:8472800-8476200	Weak transcription	Liver	Liver
46	chr4:8472800-8476800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:8473200-8475400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:8473200-8476200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:8473200-8476400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:8473200-8477000	Weak transcription	H9 Cell Line	embryonic stem cell

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