Variant report

Variant	rs3775703
Chromosome Location	chr4:143326120-143326121
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	CEBPB	chr4:143326021-143327054	IMR90	lung:	n/a	chr4:143326150-143326163
2	POLR2A	chr4:143326067-143327291	HCT-116	colon:	n/a	n/a
3	MYC	chr4:143326043-143327130	MCF10A-Er-Src	breast:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
4	STAT3	chr4:143325211-143326286	MCF10A-Er-Src	breast:	n/a	chr4:143326262-143326274 chr4:143325952-143325963
5	CEBPB	chr4:143326049-143326472	A549	lung:	n/a	chr4:143326150-143326163
6	POLR2A	chr4:143324039-143328578	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr4:143326118-143327249	ECC-1	luminal epithelium:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
8	POLR2A	chr4:143326103-143326976	ProgFib	skin:	n/a	n/a
9	POLR2A	chr4:143326007-143326920	MCF10A-Er-Src	breast:	n/a	n/a
10	TCF12	chr4:143325261-143327706	A549	lung:	n/a	chr4:143327642-143327651
11	FOS	chr4:143325212-143326250	MCF10A-Er-Src	breast:	n/a	chr4:143325403-143325414
12	STAT3	chr4:143326024-143326221	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr4:143326019-143327845	MCF10A-Er-Src	breast:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
14	MXI1	chr4:143325963-143327388	IMR90	lung:	n/a	n/a
15	MAX	chr4:143326066-143327108	HCT-116	colon:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
16	CEBPB	chr4:143325986-143326607	ECC-1	luminal epithelium:	n/a	chr4:143326150-143326163
17	MAX	chr4:143326073-143327069	A549	lung:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
18	SP1	chr4:143326110-143326510	A549	lung:	n/a	chr4:143326266-143326276 chr4:143326260-143326269 chr4:143326259-143326271 chr4:143326261-143326270 chr4:143326266-143326275
19	FOS	chr4:143326078-143326893	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr4:143325233-143326245	MCF10A-Er-Src	breast:	n/a	chr4:143325952-143325963
21	EP300	chr4:143326120-143327774	ECC-1	luminal epithelium:	n/a	chr4:143326808-143326821
22	STAT3	chr4:143326034-143326213	MCF10A-Er-Src	breast:	n/a	n/a
23	TEAD4	chr4:143326102-143327900	ECC-1	luminal epithelium:	n/a	n/a
24	MAX	chr4:143326076-143327026	ECC-1	luminal epithelium:	n/a	chr4:143326645-143326656 chr4:143326646-143326655 chr4:143326645-143326656 chr4:143326644-143326652
25	CEBPB	chr4:143325934-143326453	A549	lung:	n/a	chr4:143326150-143326163
26	STAT3	chr4:143325233-143326894	MCF10A-Er-Src	breast:	n/a	chr4:143326502-143326513 chr4:143326610-143326617 chr4:143326262-143326274 chr4:143325952-143325963 chr4:143326641-143326648
27	FOS	chr4:143325229-143327049	MCF10A-Er-Src	breast:	n/a	chr4:143325403-143325414

Variant related genes	Relation type
INPP4B	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11722756	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511267	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13128245	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13135641	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138212	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13140802	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144939	0.93[AFR][1000 genomes]
rs1489577	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1489578	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497389	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1497398	0.87[AFR][1000 genomes]
rs1565306	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1982966	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173209	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306913	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34830426	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35151914	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3775705	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775706	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775710	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775711	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822157	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6825345	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72724560	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7699598	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs881611	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs983767	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3775703	INPP4B	cis	brain	BrainEAC

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143300200-143326200	Weak transcription	Aorta	Aorta
2	chr4:143301200-143326200	Weak transcription	Gastric	stomach
3	chr4:143313000-143326200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:143320600-143326600	Active TSS	Primary T cells fromperipheralblood	blood
5	chr4:143320800-143328000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:143321000-143326800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:143321400-143326600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:143321400-143326600	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr4:143322000-143326400	Active TSS	Fetal Muscle Leg	muscle
10	chr4:143322200-143326600	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr4:143322200-143326600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr4:143322400-143326400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:143322600-143326600	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr4:143323200-143326600	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr4:143323400-143327200	Weak transcription	Small Intestine	intestine
16	chr4:143323600-143326200	Weak transcription	Ovary	ovary
17	chr4:143323600-143326400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:143323600-143326600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:143323600-143326600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:143323600-143326800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr4:143323600-143326800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:143323800-143326600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr4:143323800-143326800	Active TSS	NHLF	lung
24	chr4:143323800-143327000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:143324000-143326200	Weak transcription	Brain Germinal Matrix	brain
26	chr4:143324000-143326600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:143324000-143326800	Active TSS	Psoas Muscle	Psoas
28	chr4:143324200-143326200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:143324200-143326400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:143324200-143326400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:143324200-143326600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:143324400-143326200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:143324400-143326200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:143324400-143326200	Weak transcription	Brain Substantia Nigra	brain
35	chr4:143324400-143326200	Weak transcription	Pancreas	Pancrea
36	chr4:143324400-143326200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:143324400-143326200	Weak transcription	Right Ventricle	heart
38	chr4:143324400-143326400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:143324400-143326400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:143324400-143326400	Active TSS	Primary T cells from cord blood	blood
41	chr4:143324400-143326600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:143324400-143326600	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr4:143324400-143326600	Active TSS	HMEC	breast
44	chr4:143324400-143326600	Active TSS	HSMM	muscle
45	chr4:143324400-143326600	Active TSS	NHEK	skin
46	chr4:143324400-143326800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:143324400-143326800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:143324800-143326400	Active TSS	Dnd41	blood
49	chr4:143324800-143326600	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr4:143324800-143326600	Active TSS	HSMMtube	muscle

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