Variant report

Variant	rs11133376
Chromosome Location	chr4:56253033-56253034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

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	TBP	chr4:56253013-56253530	K562	blood:	n/a	n/a
3	POLR2A	chr4:56252931-56253357	K562	blood:	n/a	n/a
4	STAT5A	chr4:56252785-56253425	K562	blood:	n/a	n/a
5	UBTF	chr4:56252982-56253109	K562	blood:	n/a	n/a
6	NR2F2	chr4:56252928-56253413	K562	blood:	n/a	n/a
7	RCOR1	chr4:56252297-56253493	K562	blood:	n/a	n/a
8	PML	chr4:56252516-56253480	K562	blood:	n/a	n/a
9	HMGN3	chr4:56252963-56253279	K562	blood:	n/a	n/a
10	TEAD4	chr4:56252308-56253474	K562	blood:	n/a	n/a
11	POLR2A	chr4:56252899-56253397	K562	blood:	n/a	n/a
12	CEBPD	chr4:56252860-56253418	K562	blood:	n/a	n/a
13	IRF1	chr4:56252369-56253421	K562	blood:	n/a	chr4:56252943-56252952
14	CEBPB	chr4:56252801-56253365	K562	blood:	n/a	n/a
15	GATA2	chr4:56252912-56253447	K562	blood:	n/a	n/a
16	MAX	chr4:56253006-56253594	K562	blood:	n/a	n/a
17	IRF1	chr4:56253033-56253370	K562	blood:	n/a	n/a
18	KAP1	chr4:56252481-56253807	K562	blood:	n/a	n/a
19	EP300	chr4:56252867-56253493	K562	blood:	n/a	n/a
20	TAL1	chr4:56252251-56253612	K562	blood:	n/a	n/a
21	TEAD4	chr4:56252138-56253631	K562	blood:	n/a	n/a
22	CEBPB	chr4:56252208-56253404	K562	blood:	n/a	n/a
23	TRIM28	chr4:56252314-56253459	K562	blood:	n/a	n/a
24	MAZ	chr4:56252289-56253310	K562	blood:	n/a	n/a
25	TRIM28	chr4:56252944-56253306	K562	blood:	n/a	n/a
26	ATF1	chr4:56252993-56253420	K562	blood:	n/a	n/a
27	TBL1XR1	chr4:56252203-56253536	K562	blood:	n/a	n/a
28	PML	chr4:56252773-56253508	K562	blood:	n/a	n/a
29	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
30	MYC	chr4:56252214-56253662	K562	blood:	n/a	n/a
31	ZNF384	chr4:56252856-56253364	K562	blood:	n/a	n/a
32	POLR2A	chr4:56252999-56253481	K562	blood:	n/a	n/a
33	CBX3	chr4:56252237-56253759	K562	blood:	n/a	n/a
34	POLR2A	chr4:56252993-56253395	K562	blood:	n/a	n/a
35	BHLHE40	chr4:56252968-56253348	K562	blood:	n/a	n/a
36	ARID3A	chr4:56252881-56253539	K562	blood:	n/a	n/a
37	GABPA	chr4:56252988-56253438	K562	blood:	n/a	n/a
38	EP300	chr4:56253008-56253356	K562	blood:	n/a	n/a
39	MAFK	chr4:56252281-56253657	K562	blood:	n/a	n/a
40	CEBPD	chr4:56252900-56253496	K562	blood:	n/a	n/a
41	STAT5A	chr4:56252904-56253421	K562	blood:	n/a	n/a
42	IRF1	chr4:56252893-56253595	K562	blood:	n/a	chr4:56252943-56252952
43	GATA2	chr4:56252958-56253314	K562	blood:	n/a	n/a
44	JUND	chr4:56252192-56253415	K562	blood:	n/a	n/a
45	GATA1	chr4:56252572-56253634	PBDE	blood:	n/a	n/a
46	RCOR1	chr4:56252286-56253424	K562	blood:	n/a	n/a
47	GATA1	chr4:56252995-56253381	K562	blood:	n/a	n/a
48	MAFF	chr4:56252310-56253379	K562	blood:	n/a	n/a
49	JUN	chr4:56253032-56253405	K562	blood:	n/a	n/a
50	MXI1	chr4:56252578-56253359	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
ENSG00000128039	Chromatin interaction
ENSG00000134851	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10002541	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs10005989	0.91[CEU][hapmap]
rs10016506	0.84[JPT][hapmap]
rs10026692	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1011095	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133379	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs11133383	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs11133399	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs1128141	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11726609	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11735267	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs11931061	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11939815	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs13102385	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs13121235	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap]
rs1522106	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes]
rs1522111	0.91[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs1873092	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2177127	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2177129	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2412643	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2412646	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap]
rs28665088	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28726308	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3736544	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs3805147	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs3805154	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs3817444	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs4580704	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs473005	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs480479	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4865010	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs501679	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs564762	0.82[ASN][1000 genomes]
rs576779	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6554286	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs6811520	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs6812042	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs6815516	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs6819649	0.84[EUR][1000 genomes]
rs6824955	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs6832769	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs6837710	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs6850524	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs6851838	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs6853192	0.88[CEU][hapmap]
rs726967	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs7660054	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7667849	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7673908	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7684810	0.88[CEU][hapmap]
rs819271	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9312662	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs9993675	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9997288	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]

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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