Variant report

Variant	rs62305201
Chromosome Location	chr4:56252945-56252946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr4:56252129-56253757	K562	blood:	n/a	n/a
2	POLR2A	chr4:56252931-56253357	K562	blood:	n/a	n/a
3	STAT5A	chr4:56252785-56253425	K562	blood:	n/a	n/a
4	NR2F2	chr4:56252928-56253413	K562	blood:	n/a	n/a
5	RCOR1	chr4:56252297-56253493	K562	blood:	n/a	n/a
6	PML	chr4:56252516-56253480	K562	blood:	n/a	n/a
7	TEAD4	chr4:56252308-56253474	K562	blood:	n/a	n/a
8	YY1	chr4:56252738-56252981	K562	blood:	n/a	n/a
9	POLR2A	chr4:56252899-56253397	K562	blood:	n/a	n/a
10	CEBPD	chr4:56252860-56253418	K562	blood:	n/a	n/a
11	IRF1	chr4:56252369-56253421	K562	blood:	n/a	chr4:56252943-56252952
12	CEBPB	chr4:56252801-56253365	K562	blood:	n/a	n/a
13	GATA2	chr4:56252912-56253447	K562	blood:	n/a	n/a
14	KAP1	chr4:56252481-56253807	K562	blood:	n/a	n/a
15	EP300	chr4:56252867-56253493	K562	blood:	n/a	n/a
16	TAL1	chr4:56252251-56253612	K562	blood:	n/a	n/a
17	TEAD4	chr4:56252138-56253631	K562	blood:	n/a	n/a
18	CEBPB	chr4:56252208-56253404	K562	blood:	n/a	n/a
19	TRIM28	chr4:56252314-56253459	K562	blood:	n/a	n/a
20	MAZ	chr4:56252289-56253310	K562	blood:	n/a	n/a
21	TRIM28	chr4:56252944-56253306	K562	blood:	n/a	n/a
22	BACH1	chr4:56252916-56252968	K562	blood:	n/a	n/a
23	TBL1XR1	chr4:56252203-56253536	K562	blood:	n/a	n/a
24	PML	chr4:56252773-56253508	K562	blood:	n/a	n/a
25	GATA1	chr4:56250710-56254022	K562	blood:	n/a	chr4:56251408-56251418 chr4:56251410-56251420 chr4:56251410-56251417 chr4:56251405-56251421 chr4:56251410-56251417 chr4:56251410-56251417 chr4:56251407-56251419 chr4:56251646-56251653
26	MYC	chr4:56252214-56253662	K562	blood:	n/a	n/a
27	ZNF384	chr4:56252856-56253364	K562	blood:	n/a	n/a
28	CBX3	chr4:56252237-56253759	K562	blood:	n/a	n/a
29	ARID3A	chr4:56252881-56253539	K562	blood:	n/a	n/a
30	MAFK	chr4:56252281-56253657	K562	blood:	n/a	n/a
31	CEBPD	chr4:56252900-56253496	K562	blood:	n/a	n/a
32	STAT5A	chr4:56252904-56253421	K562	blood:	n/a	n/a
33	IRF1	chr4:56252893-56253595	K562	blood:	n/a	chr4:56252943-56252952
34	JUND	chr4:56252192-56253415	K562	blood:	n/a	n/a
35	GATA1	chr4:56252572-56253634	PBDE	blood:	n/a	n/a
36	RCOR1	chr4:56252286-56253424	K562	blood:	n/a	n/a
37	MAFF	chr4:56252310-56253379	K562	blood:	n/a	n/a
38	MXI1	chr4:56252578-56253359	K562	blood:	n/a	n/a
39	TBL1XR1	chr4:56252944-56253411	K562	blood:	n/a	n/a
40	ZNF274	chr4:56252507-56253406	K562	blood:	n/a	n/a
41	CCNT2	chr4:56252816-56253441	K562	blood:	n/a	n/a
42	NFYA	chr4:56252246-56253390	K562	blood:	n/a	chr4:56252421-56252439
43	MYC	chr4:56252286-56253587	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56211308..56214746-chr4:56245753..56253172,10	K562	blood:
2	chr4:56252554..56257772-chr4:56259709..56263846,8	MCF-7	breast:
3	chr4:56249230..56252021-chr4:56252928..56255914,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRD5A3-1	chr4:56252510-56254858	XLOC_003544
2	lnc-SRD5A3-1	chr4:56252510-56253958	XLOC_003544
3	lnc-CLOCK-1	chr4:56252870-56253057	ENSG00000249700.4
4	lnc-CLOCK-1	chr4:56252945-56253704	ENSG00000249700.4

No data

Variant related genes	Relation type
SRD5A3-AS1	TF binding region
ENSG00000273257	TF binding region
ENSG00000249700	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000128039	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10010762	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10021233	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10024928	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17776975	0.86[ASN][1000 genomes]
rs1818460	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1818461	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2538	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28609134	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3087606	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4089487	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4455482	0.98[ASN][1000 genomes]
rs475465	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs476184	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs482114	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs483978	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs496055	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs499110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs525271	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs552792	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs552950	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556072	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56139168	0.86[ASN][1000 genomes]
rs572428	0.96[ASN][1000 genomes]
rs572553	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs573960	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs576732	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58176292	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58506276	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59648459	0.93[ASN][1000 genomes]
rs60097207	0.86[ASN][1000 genomes]
rs62303681	0.86[ASN][1000 genomes]
rs62305200	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62305202	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305206	1.00[ASN][1000 genomes]
rs62306207	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554275	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs693367	0.96[ASN][1000 genomes]
rs7340797	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs819203	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs819266	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs819267	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs819268	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs819269	0.82[AMR][1000 genomes]
rs819270	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs861029	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs880358	0.86[ASN][1000 genomes]
rs9312660	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56240400-56259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:56248000-56254000	Weak transcription	Spleen	Spleen
4	chr4:56248000-56259400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:56248200-56261400	Weak transcription	Aorta	Aorta
6	chr4:56249200-56261200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:56251200-56253600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:56251400-56254200	Enhancers	HepG2	liver
9	chr4:56251400-56254400	Flanking Active TSS	K562	blood
10	chr4:56251800-56253600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:56251800-56255000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr4:56252200-56256800	Weak transcription	Fetal Intestine Small	intestine
13	chr4:56252400-56253600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:56252400-56261600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:56252600-56253400	Weak transcription	Pancreas	Pancrea
16	chr4:56252600-56257400	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:56252600-56257400	Weak transcription	Brain Substantia Nigra	brain

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