Variant report

Variant	rs4109037
Chromosome Location	chr4:57775609-57775610
allele	A/T
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	POLR2A	chr4:57774832-57775766	GM12878	blood:	n/a	n/a
2	MAX	chr4:57773747-57775766	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:57774549-57775761	Hela-S3	cervix:	n/a	n/a
4	MAX	chr4:57774532-57776163	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr4:57774474-57775981	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:57774393-57775646	GM12878	blood:	n/a	n/a
7	REST	chr4:57773926-57775638	MCF-7	breast:	n/a	chr4:57774480-57774489 chr4:57774581-57774591 chr4:57774720-57774734 chr4:57774122-57774135 chr4:57774480-57774493 chr4:57774118-57774138
8	REST	chr4:57775158-57775731	PANC-1	pancreas:	n/a	n/a
9	CTCF	chr4:57775500-57775650	AG10803	skin:	n/a	n/a
10	POLR2A	chr4:57774585-57775788	GM12892	blood:	n/a	n/a
11	MYC	chr4:57775477-57775765	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr4:57775425-57775831	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr4:57774437-57775807	HepG2	liver:	n/a	n/a
14	HA-E2F1	chr4:57773647-57775798	MCF-7	breast:	n/a	chr4:57774165-57774175 chr4:57774582-57774592 chr4:57774574-57774584
15	UBTF	chr4:57773999-57775832	K562	blood:	n/a	n/a
16	YY1	chr4:57774665-57775786	GM12892	blood:	n/a	chr4:57774981-57774992
17	SIN3AK20	chr4:57775180-57775660	H1-hESC	embryonic stem cell:	n/a	n/a
18	BCLAF1	chr4:57774722-57775828	GM12878	blood:	n/a	chr4:57774933-57774946 chr4:57774937-57774950 chr4:57775290-57775298 chr4:57774979-57774992
19	YY1	chr4:57775303-57775620	K562	blood:	n/a	n/a
20	MAX	chr4:57773756-57775706	NB4	blood:	n/a	n/a
21	TBP	chr4:57775351-57775877	GM12878	blood:	n/a	n/a
22	MXI1	chr4:57775434-57775742	H1-hESC	embryonic stem cell:	n/a	n/a
23	MXI1	chr4:57773345-57776166	IMR90	lung:	n/a	n/a
24	CHD1	chr4:57774719-57776234	GM12878	blood:	n/a	n/a
25	TEAD4	chr4:57775231-57776110	K562	blood:	n/a	n/a
26	TAL1	chr4:57775353-57775874	K562	blood:	n/a	n/a
27	POLR2A	chr4:57773922-57775695	GM19193	blood:	n/a	n/a
28	POLR2A	chr4:57774774-57775650	MCF10A-Er-Src	breast:	n/a	n/a
29	MYC	chr4:57775520-57775720	H1-hESC	embryonic stem cell:	n/a	n/a
30	MXI1	chr4:57773723-57775676	HepG2	liver:	n/a	n/a
31	YY1	chr4:57775263-57775666	GM12892	blood:	n/a	n/a
32	UBTF	chr4:57773819-57776233	K562	blood:	n/a	n/a
33	MAX	chr4:57774809-57775879	A549	lung:	n/a	n/a
34	POLR2A	chr4:57775094-57776108	Hela-S3	cervix:	n/a	n/a
35	TEAD4	chr4:57775220-57775751	ECC-1	luminal epithelium:	n/a	n/a
36	MAX	chr4:57773763-57775621	K562	blood:	n/a	n/a
37	YY1	chr4:57775098-57776077	H1-hESC	embryonic stem cell:	n/a	n/a
38	EP300	chr4:57775390-57775997	GM12878	blood:	n/a	n/a
39	TBP	chr4:57775162-57776074	H1-hESC	embryonic stem cell:	n/a	n/a
40	MTA3	chr4:57775058-57775719	GM12878	blood:	n/a	n/a
41	YY1	chr4:57775218-57775667	A549	lung:	n/a	n/a
42	SMC3	chr4:57775390-57775749	Hela-S3	cervix:	n/a	n/a
43	ELF1	chr4:57773783-57775651	GM12878	blood:	n/a	chr4:57775032-57775041 chr4:57774652-57774661 chr4:57775031-57775042 chr4:57774439-57774451
44	RFX5	chr4:57775307-57775623	GM12878	blood:	n/a	n/a
45	YY1	chr4:57773980-57775700	K562	blood:	n/a	chr4:57774585-57774596 chr4:57774981-57774992 chr4:57774127-57774141 chr4:57774164-57774178 chr4:57774174-57774185 chr4:57774423-57774437 chr4:57774168-57774182 chr4:57774097-57774108
46	REST	chr4:57773890-57775648	U87	brain:	n/a	chr4:57774480-57774489 chr4:57773900-57773913 chr4:57774581-57774591 chr4:57774720-57774734 chr4:57774122-57774135 chr4:57774480-57774493 chr4:57774118-57774138
47	STAT5A	chr4:57774766-57775799	GM12878	blood:	n/a	n/a
48	MYC	chr4:57773776-57776081	NB4	blood:	n/a	n/a
49	MXI1	chr4:57775096-57775737	Hela-S3	cervix:	n/a	n/a
50	IRF1	chr4:57774897-57776326	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57772839..57777394-chr4:57841397..57848240,17	K562	blood:
2	chr4:57301355..57303854-chr4:57773620..57776020,4	MCF-7	breast:
3	chr4:57302175..57303989-chr4:57773484..57775623,2	MCF-7	breast:
4	chr4:57771688..57776264-chr4:57841866..57845328,7	MCF-7	breast:
5	chr4:57774412..57776864-chr4:57776976..57782053,6	K562	blood:
6	chr4:57299951..57301849-chr4:57773604..57776000,3	K562	blood:
7	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:

Variant related genes	Relation type
REST	TF binding region
ENSG00000128050	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000084092	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10016108	1.00[CHB][hapmap]
rs11133472	1.00[CHB][hapmap]
rs11573041	1.00[CHB][hapmap]
rs11573128	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs11730396	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11732394	1.00[CHB][hapmap]
rs13125082	1.00[CHB][hapmap]
rs13146090	1.00[CHB][hapmap]
rs13146153	1.00[CHB][hapmap]
rs1618761	1.00[CHB][hapmap]
rs17087358	1.00[CHB][hapmap]
rs17183291	1.00[CHB][hapmap]
rs1718846	1.00[CHB][hapmap]
rs1718848	1.00[CHB][hapmap]
rs41495551	1.00[CHB][hapmap]
rs4865176	1.00[CHB][hapmap]
rs4865177	1.00[CHB][hapmap]
rs62308153	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6839166	0.83[AMR][1000 genomes]
rs7656865	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv822562	chr4:57768655-57779715	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3374947	chr4:57773220-57776168	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	esv3389347	chr4:57773345-57775893	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57772800-57776200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:57773000-57776000	Active TSS	Rectal Smooth Muscle	rectum
3	chr4:57773200-57775800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:57773200-57776000	Active TSS	A549	lung
5	chr4:57773200-57776000	Active TSS	HMEC	breast
6	chr4:57773200-57776200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:57773200-57776200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:57773200-57776400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr4:57773200-57776600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:57773200-57776600	Active TSS	Aorta	Aorta
11	chr4:57773200-57776800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:57773400-57775800	Active TSS	Esophagus	oesophagus
13	chr4:57773400-57776000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:57773400-57776000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:57773400-57776000	Active TSS	Duodenum Mucosa	Duodenum
16	chr4:57773400-57776200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr4:57773400-57776200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:57773400-57776200	Active TSS	Brain Anterior Caudate	brain
19	chr4:57773400-57776200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr4:57773400-57776200	Active TSS	Ovary	ovary
21	chr4:57773400-57776600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:57773400-57776800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:57773400-57776800	Active TSS	Psoas Muscle	Psoas
24	chr4:57773600-57775800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:57773600-57775800	Active TSS	Brain Angular Gyrus	brain
26	chr4:57773600-57775800	Active TSS	Brain Cingulate Gyrus	brain
27	chr4:57773600-57775800	Active TSS	Brain Hippocampus Middle	brain
28	chr4:57773600-57775800	Active TSS	Gastric	stomach
29	chr4:57773600-57775800	Active TSS	Placenta Amnion	Placenta Amnion
30	chr4:57773600-57775800	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr4:57773600-57776000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr4:57773600-57776000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:57773600-57776000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:57773600-57776000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr4:57773600-57776000	Active TSS	Fetal Lung	lung
36	chr4:57773600-57776000	Active TSS	Left Ventricle	heart
37	chr4:57773600-57776000	Active TSS	Pancreas	Pancrea
38	chr4:57773600-57776000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr4:57773600-57776200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:57773600-57776200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:57773600-57776200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:57773600-57776200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:57773600-57776200	Active TSS	Colon Smooth Muscle	Colon
44	chr4:57773600-57776200	Active TSS	Fetal Muscle Trunk	muscle
45	chr4:57773600-57776200	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr4:57773600-57776200	Active TSS	Thymus	Thymus
47	chr4:57773600-57776400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:57773600-57776400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr4:57773600-57776400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr4:57773600-57776400	Active TSS	Fetal Muscle Leg	muscle

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