Variant report

Variant	rs3775704
Chromosome Location	chr4:143326851-143326852
allele	A/G
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	USF1	chr4:143326399-143326924	ECC-1	luminal epithelium:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
2	CEBPB	chr4:143326021-143327054	IMR90	lung:	n/a	chr4:143326150-143326163
3	POLR2A	chr4:143326067-143327291	HCT-116	colon:	n/a	n/a
4	MYC	chr4:143326043-143327130	MCF10A-Er-Src	breast:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
5	WRNIP1	chr4:143326456-143326985	GM12878	blood:	n/a	n/a
6	CHD2	chr4:143326300-143326980	GM12878	blood:	n/a	n/a
7	STAT3	chr4:143326488-143326885	MCF10A-Er-Src	breast:	n/a	chr4:143326502-143326513 chr4:143326610-143326617 chr4:143326641-143326648
8	EP300	chr4:143326339-143327167	GM12878	blood:	n/a	chr4:143326808-143326821
9	STAT3	chr4:143326468-143326869	MCF10A-Er-Src	breast:	n/a	chr4:143326502-143326513 chr4:143326610-143326617 chr4:143326641-143326648
10	IKZF1	chr4:143326349-143327070	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:143324039-143328578	MCF10A-Er-Src	breast:	n/a	n/a
12	MAX	chr4:143326118-143327249	ECC-1	luminal epithelium:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
13	POLR2A	chr4:143326103-143326976	ProgFib	skin:	n/a	n/a
14	USF1	chr4:143326419-143326897	A549	lung:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
15	FOXA1	chr4:143326697-143327028	T-47D	breast:	n/a	n/a
16	POLR2A	chr4:143326007-143326920	MCF10A-Er-Src	breast:	n/a	n/a
17	TCF12	chr4:143325261-143327706	A549	lung:	n/a	chr4:143327642-143327651
18	SP1	chr4:143326555-143327258	A549	lung:	n/a	n/a
19	RUNX3	chr4:143326448-143326946	GM12878	blood:	n/a	n/a
20	USF1	chr4:143326418-143326869	A549	lung:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
21	EBF1	chr4:143326248-143327165	GM12878	blood:	n/a	chr4:143326580-143326591 chr4:143327120-143327130
22	MAX	chr4:143326312-143327292	NB4	blood:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
23	USF1	chr4:143326216-143327108	HCT-116	colon:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
24	FOXA1	chr4:143326687-143327048	T-47D	breast:	n/a	n/a
25	MXI1	chr4:143326332-143326920	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:143326273-143326914	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr4:143326219-143327162	HCT-116	colon:	n/a	n/a
28	MYC	chr4:143326019-143327845	MCF10A-Er-Src	breast:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
29	SPI1	chr4:143326344-143327236	HL-60	blood:	n/a	chr4:143327016-143327025 chr4:143326608-143326615 chr4:143327017-143327024
30	RCOR1	chr4:143326549-143326872	GM12878	blood:	n/a	n/a
31	MXI1	chr4:143325963-143327388	IMR90	lung:	n/a	n/a
32	NRF1	chr4:143326753-143326886	GM12878	blood:	n/a	n/a
33	GATA3	chr4:143326620-143326946	T-47D	breast:	n/a	n/a
34	MAX	chr4:143326066-143327108	HCT-116	colon:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
35	EP300	chr4:143326501-143326973	GM12878	blood:	n/a	chr4:143326808-143326821
36	MAX	chr4:143326073-143327069	A549	lung:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
37	POLR2A	chr4:143326278-143327022	IMR90	lung:	n/a	n/a
38	USF2	chr4:143326425-143326867	GM12878	blood:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655
39	POLR2A	chr4:143326620-143326917	MCF-7	breast:	n/a	n/a
40	FOS	chr4:143326078-143326893	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr4:143326242-143327029	U87	brain:	n/a	n/a
42	KAP1	chr4:143326346-143327707	U2OS	brain:	n/a	n/a
43	BCL11A	chr4:143326567-143326904	GM12878	blood:	n/a	n/a
44	MAX	chr4:143326418-143327010	GM12878	blood:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
45	USF1	chr4:143326480-143326893	A549	lung:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
46	NFIC	chr4:143326488-143326929	GM12878	blood:	n/a	n/a
47	EP300	chr4:143326120-143327774	ECC-1	luminal epithelium:	n/a	chr4:143326808-143326821
48	FOXM1	chr4:143326822-143327864	ECC-1	luminal epithelium:	n/a	n/a
49	USF1	chr4:143326324-143327009	ECC-1	luminal epithelium:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
50	FOS	chr4:143326467-143326977	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143326731..143329100-chr4:143388048..143390704,2	MCF-7	breast:
2	chr4:143326578..143329374-chr4:143334403..143336752,2	MCF-7	breast:

Variant related genes	Relation type
INPP4B	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10519644	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11930321	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11944462	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11944503	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12499785	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12500699	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17016123	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2130251	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2130252	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2171756	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28555074	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28588752	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4435818	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4476678	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4551010	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4566727	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60479909	0.84[ASN][1000 genomes]
rs61515079	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66511868	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66537547	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66941440	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67001118	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67013221	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67111439	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67440355	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67710427	0.81[ASN][1000 genomes]
rs67760986	0.86[ASN][1000 genomes]
rs67947007	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6820234	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6829034	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6839769	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6851331	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6854342	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72724524	0.81[ASN][1000 genomes]
rs72724531	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72724534	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72941192	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72944948	0.92[EUR][1000 genomes];0.92[ASN][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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv968011	chr4:143325315-143333139	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143320800-143328000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:143323400-143327200	Weak transcription	Small Intestine	intestine
3	chr4:143323800-143327000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:143324800-143327600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:143325200-143327000	Active TSS	Rectal Smooth Muscle	rectum
6	chr4:143325400-143327000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr4:143325400-143327600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr4:143325600-143327200	Active TSS	Brain Angular Gyrus	brain
9	chr4:143326000-143327400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:143326200-143327000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr4:143326200-143327000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:143326200-143327000	Active TSS	Aorta	Aorta
13	chr4:143326200-143327000	Active TSS	Brain Cingulate Gyrus	brain
14	chr4:143326200-143327000	Active TSS	Ovary	ovary
15	chr4:143326200-143327000	Enhancers	Spleen	Spleen
16	chr4:143326200-143327000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr4:143326200-143327200	Active TSS	Fetal Muscle Trunk	muscle
18	chr4:143326200-143327200	Active TSS	Left Ventricle	heart
19	chr4:143326200-143327600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:143326200-143327600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:143326400-143327000	Enhancers	H9 Cell Line	embryonic stem cell
22	chr4:143326400-143327000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr4:143326400-143327000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr4:143326400-143327000	Enhancers	Primary B cells from peripheral blood	blood
25	chr4:143326400-143327000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:143326400-143327000	Flanking Active TSS	Placenta	Placenta
27	chr4:143326400-143327000	Flanking Active TSS	Fetal Thymus	thymus
28	chr4:143326400-143327000	Flanking Active TSS	Thymus	Thymus
29	chr4:143326400-143327000	Active TSS	GM12878-XiMat	blood
30	chr4:143326400-143327000	Flanking Active TSS	HUVEC	blood vessel
31	chr4:143326400-143327200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr4:143326400-143327200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr4:143326400-143327200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr4:143326400-143327200	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr4:143326400-143327400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr4:143326400-143327400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr4:143326400-143327400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr4:143326400-143327600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:143326400-143327600	Flanking Active TSS	Dnd41	blood
40	chr4:143326400-143327800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr4:143326400-143327800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:143326400-143327800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:143326400-143327800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:143326400-143328000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:143326400-143328600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr4:143326400-143329000	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr4:143326400-143330400	Enhancers	Hela-S3	cervix
48	chr4:143326600-143327000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:143326600-143327000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:143326600-143327000	Flanking Active TSS	Adipose Nuclei	Adipose

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