Variant report

Variant	rs7696969
Chromosome Location	chr4:143326714-143326715
allele	G/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	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	MAX	chr4:143326644-143326844	H1-hESC	embryonic stem cell:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
12	SPI1	chr4:143326417-143326771	GM12891	blood:	n/a	chr4:143326608-143326615
13	POLR2A	chr4:143324039-143328578	MCF10A-Er-Src	breast:	n/a	n/a
14	MAX	chr4:143326118-143327249	ECC-1	luminal epithelium:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
15	TBP	chr4:143326391-143326843	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:143326103-143326976	ProgFib	skin:	n/a	n/a
17	USF1	chr4:143326536-143326738	H1-hESC	embryonic stem cell:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
18	USF1	chr4:143326419-143326897	A549	lung:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
19	FOXA1	chr4:143326697-143327028	T-47D	breast:	n/a	n/a
20	POLR2A	chr4:143326007-143326920	MCF10A-Er-Src	breast:	n/a	n/a
21	TCF12	chr4:143325261-143327706	A549	lung:	n/a	chr4:143327642-143327651
22	USF1	chr4:143326404-143326831	A549	lung:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
23	BHLHE40	chr4:143326598-143326796	K562	blood:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655
24	SP1	chr4:143326555-143327258	A549	lung:	n/a	n/a
25	RUNX3	chr4:143326448-143326946	GM12878	blood:	n/a	n/a
26	USF1	chr4:143326418-143326869	A549	lung:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
27	EBF1	chr4:143326248-143327165	GM12878	blood:	n/a	chr4:143326580-143326591 chr4:143327120-143327130
28	MAX	chr4:143326312-143327292	NB4	blood:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
29	STAT3	chr4:143326475-143326809	MCF10A-Er-Src	breast:	n/a	chr4:143326502-143326513 chr4:143326610-143326617 chr4:143326641-143326648
30	YY1	chr4:143326224-143326845	HCT-116	colon:	n/a	chr4:143326261-143326272
31	USF1	chr4:143326216-143327108	HCT-116	colon:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
32	USF1	chr4:143326561-143326737	HepG2	liver:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
33	FOXA1	chr4:143326687-143327048	T-47D	breast:	n/a	n/a
34	MXI1	chr4:143326332-143326920	GM12878	blood:	n/a	n/a
35	POLR2A	chr4:143326273-143326914	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr4:143326223-143326849	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr4:143326219-143327162	HCT-116	colon:	n/a	n/a
38	BCL11A	chr4:143326597-143326837	GM12878	blood:	n/a	n/a
39	MYC	chr4:143326019-143327845	MCF10A-Er-Src	breast:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
40	SPI1	chr4:143326344-143327236	HL-60	blood:	n/a	chr4:143327016-143327025 chr4:143326608-143326615 chr4:143327017-143327024
41	RCOR1	chr4:143326549-143326872	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:143326638-143326790	HUVEC	blood vessel:	n/a	n/a
43	MXI1	chr4:143325963-143327388	IMR90	lung:	n/a	n/a
44	GATA3	chr4:143326620-143326946	T-47D	breast:	n/a	n/a
45	STAT3	chr4:143326627-143326833	GM12878	blood:	n/a	chr4:143326641-143326648
46	MAX	chr4:143326066-143327108	HCT-116	colon:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
47	EP300	chr4:143326501-143326973	GM12878	blood:	n/a	chr4:143326808-143326821
48	MAX	chr4:143326073-143327069	A549	lung:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
49	USF1	chr4:143326526-143326759	GM12878	blood:	n/a	chr4:143326645-143326654 chr4:143326646-143326655 chr4:143326646-143326655 chr4:143326644-143326655
50	CHD1	chr4:143326321-143326848	GM12878	blood:	n/a	n/a

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

Variant related genes	Relation type
INPP4B	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10006795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10006884	0.83[AMR][1000 genomes]
rs10006971	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13151359	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1391097	0.81[GIH][hapmap]
rs1497401	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17016027	0.81[GIH][hapmap]
rs1982965	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2173208	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2322549	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62328321	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6812973	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6822835	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7696969	LSM6	cis	cerebellum	SCAN
rs7696969	ZNF827	cis	parietal	SCAN
rs7696969	TM4SF5	trans	cerebellum	SCAN

Chromatin state (count:122 , 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	chr4:143321000-143326800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:143323400-143327200	Weak transcription	Small Intestine	intestine
4	chr4:143323600-143326800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:143323600-143326800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:143323800-143326800	Active TSS	NHLF	lung
7	chr4:143323800-143327000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:143324000-143326800	Active TSS	Psoas Muscle	Psoas
9	chr4:143324400-143326800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:143324400-143326800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:143324800-143326800	Active TSS	A549	lung
12	chr4:143324800-143326800	Active TSS	NHDF-Ad	bronchial
13	chr4:143324800-143327600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:143325200-143326800	Active TSS	Stomach Smooth Muscle	stomach
15	chr4:143325200-143327000	Active TSS	Rectal Smooth Muscle	rectum
16	chr4:143325400-143326800	Active TSS	Brain Hippocampus Middle	brain
17	chr4:143325400-143327000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr4:143325400-143327600	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr4:143325600-143326800	Active TSS	Fetal Kidney	kidney
20	chr4:143325600-143327200	Active TSS	Brain Angular Gyrus	brain
21	chr4:143326000-143326800	Active TSS	Brain Anterior Caudate	brain
22	chr4:143326000-143326800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr4:143326000-143326800	Active TSS	Fetal Intestine Large	intestine
24	chr4:143326000-143326800	Active TSS	Fetal Lung	lung
25	chr4:143326000-143327400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:143326200-143326800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr4:143326200-143326800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:143326200-143326800	Active TSS	Colonic Mucosa	Colon
29	chr4:143326200-143326800	Active TSS	Colon Smooth Muscle	Colon
30	chr4:143326200-143326800	Active TSS	Esophagus	oesophagus
31	chr4:143326200-143326800	Active TSS	Right Ventricle	heart
32	chr4:143326200-143327000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr4:143326200-143327000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:143326200-143327000	Active TSS	Aorta	Aorta
35	chr4:143326200-143327000	Active TSS	Brain Cingulate Gyrus	brain
36	chr4:143326200-143327000	Active TSS	Ovary	ovary
37	chr4:143326200-143327000	Enhancers	Spleen	Spleen
38	chr4:143326200-143327000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr4:143326200-143327200	Active TSS	Fetal Muscle Trunk	muscle
40	chr4:143326200-143327200	Active TSS	Left Ventricle	heart
41	chr4:143326200-143327600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:143326200-143327600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:143326400-143326800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr4:143326400-143326800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr4:143326400-143326800	Bivalent/Poised TSS	Fetal Brain Male	brain
46	chr4:143326400-143326800	Active TSS	Fetal Brain Female	brain
47	chr4:143326400-143326800	Active TSS	Stomach Mucosa	stomach
48	chr4:143326400-143327000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr4:143326400-143327000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr4:143326400-143327000	Flanking Active TSS	Primary B cells from cord blood	blood

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