Variant report

Variant	rs760307
Chromosome Location	chr2:191208795-191208796
allele	C/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	FOXA1	chr2:191208225-191209198	HepG2	liver:	n/a	n/a
2	CHD2	chr2:191208221-191209140	Hela-S3	cervix:	n/a	n/a
3	ZBTB7A	chr2:191208086-191209167	ECC-1	luminal epithelium:	n/a	chr2:191208353-191208361
4	ELF1	chr2:191207890-191209226	GM12878	blood:	n/a	chr2:191208376-191208388 chr2:191208332-191208344 chr2:191208422-191208434 chr2:191208381-191208390
5	POLR2A	chr2:191208158-191209165	GM18951	blood:	n/a	n/a
6	TBP	chr2:191208381-191209114	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:191208058-191209284	IMR90	lung:	n/a	n/a
8	MAX	chr2:191207877-191209437	HCT-116	colon:	n/a	chr2:191208347-191208356
9	MAX	chr2:191208079-191209187	SK-N-SH	brain:	n/a	chr2:191208347-191208356
10	MAX	chr2:191207884-191209428	A549	lung:	n/a	chr2:191208347-191208356
11	CTCF	chr2:191208740-191208890	GM12869	blood:	n/a	n/a
12	MAX	chr2:191207970-191209346	HepG2	liver:	n/a	chr2:191208347-191208356
13	CTCF	chr2:191208759-191209286	IMR90	lung:	n/a	chr2:191209102-191209118
14	SMC3	chr2:191208441-191209614	SK-N-SH	brain:	n/a	chr2:191208655-191208665
15	PML	chr2:191207914-191209349	GM12878	blood:	n/a	n/a
16	YY1	chr2:191208535-191209017	GM12891	blood:	n/a	chr2:191208597-191208611 chr2:191208546-191208560
17	CTCF	chr2:191208794-191209235	MCF-7	breast:	n/a	chr2:191209102-191209118
18	CTCF	chr2:191208634-191209257	H1-hESC	embryonic stem cell:	n/a	chr2:191209102-191209118
19	YY1	chr2:191208668-191209238	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:191207977-191208834	Hela-S3	cervix:	n/a	n/a
21	MXI1	chr2:191208456-191209215	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr2:191208122-191209285	SK-N-SH	brain:	n/a	chr2:191208347-191208356
23	POLR2A	chr2:191208024-191209006	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr2:191208488-191208801	H1-hESC	embryonic stem cell:	n/a	n/a
25	YY1	chr2:191208659-191209164	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr2:191208024-191208996	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr2:191207854-191209161	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr2:191208012-191208889	HCT-116	colon:	n/a	n/a
29	CTCF	chr2:191208786-191208843	GM10248	blood:	n/a	n/a
30	MAX	chr2:191207992-191209277	NB4	blood:	n/a	chr2:191208347-191208356
31	BHLHE40	chr2:191208274-191209297	HepG2	liver:	n/a	chr2:191208546-191208562 chr2:191208917-191208933
32	POLR2A	chr2:191208015-191209192	Hela-S3	cervix:	n/a	n/a
33	YY1	chr2:191208374-191209059	GM12878	blood:	n/a	chr2:191208597-191208611 chr2:191208421-191208435 chr2:191208546-191208560 chr2:191208427-191208436 chr2:191208424-191208433 chr2:191208422-191208436
34	MBD4	chr2:191207883-191209386	HepG2	liver:	n/a	n/a
35	CEBPB	chr2:191208535-191209107	HepG2	liver:	n/a	n/a
36	MAZ	chr2:191208546-191209159	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:191208064-191208993	A549	lung:	n/a	n/a
38	MYC	chr2:191208173-191208894	MCF10A-Er-Src	breast:	n/a	chr2:191208347-191208356
39	MAX	chr2:191207959-191209312	A549	lung:	n/a	chr2:191208347-191208356
40	RFX5	chr2:191208217-191209747	Hela-S3	cervix:	n/a	n/a
41	CEBPB	chr2:191208532-191208835	IMR90	lung:	n/a	n/a
42	MXI1	chr2:191208194-191209291	HepG2	liver:	n/a	n/a
43	CHD1	chr2:191208631-191209121	GM12878	blood:	n/a	n/a
44	POLR2A	chr2:191207896-191209102	Hela-S3	cervix:	n/a	n/a
45	MAX	chr2:191208298-191209208	HepG2	liver:	n/a	chr2:191208347-191208356
46	POLR2A	chr2:191208198-191209243	HepG2	liver:	n/a	n/a
47	RAD21	chr2:191208748-191209355	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr2:191208181-191208964	A549	lung:	n/a	n/a
49	MAX	chr2:191208025-191209245	Hela-S3	cervix:	n/a	chr2:191208347-191208356
50	ZNF143	chr2:191208384-191209188	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191207151..191209417-chr2:191272894..191274824,2	MCF-7	breast:
2	chr2:191184511..191186549-chr2:191207772..191209465,2	MCF-7	breast:

Variant related genes	Relation type
INPP1	TF binding region
ENSG00000198130	Chromatin interaction
ENSG00000151690	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1058180	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs10931450	0.81[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11683636	0.89[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs11684995	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs11685119	0.81[EUR][1000 genomes]
rs11689196	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11692448	0.95[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs11894667	0.91[MEX][hapmap]
rs1366672	0.82[TSI][hapmap]
rs16832420	0.95[CEU][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs16832456	0.82[TSI][hapmap]
rs16832512	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs176712	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs188339	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs2016037	0.89[EUR][1000 genomes]
rs2028431	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2067398	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2067402	0.81[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2067411	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2067418	0.90[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2067419	0.90[CEU][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2067454	0.82[EUR][1000 genomes]
rs2099127	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2136567	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2244076	0.81[CEU][hapmap]
rs2271270	0.82[TSI][hapmap]
rs2354871	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562796	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs2582742	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs2582753	0.81[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2582762	0.82[TSI][hapmap]
rs291407	0.82[TSI][hapmap]
rs291418	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs291451	0.82[MEX][hapmap];0.82[TSI][hapmap]
rs291463	0.80[EUR][1000 genomes]
rs3791789	0.82[TSI][hapmap]
rs3791792	0.81[EUR][1000 genomes]
rs3791800	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs3791805	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3791806	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3791813	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3791815	0.81[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4146044	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4853684	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap]
rs4853687	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs4853689	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4853693	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55684836	0.80[EUR][1000 genomes]
rs55742982	0.81[EUR][1000 genomes]
rs57199157	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58400804	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60469543	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60986316	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61038868	0.81[EUR][1000 genomes]
rs6723792	0.81[EUR][1000 genomes]
rs6752703	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6753459	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs67791002	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs713425	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs72627905	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72627906	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7562807	0.84[MEX][hapmap];0.82[TSI][hapmap]
rs7567973	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7599085	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3405665	chr2:191207532-191210080	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs760307	INPP1	Cis_1M	lymphoblastoid	RTeQTL
rs760307	INPP1	cis	cerebellum	SCAN
rs760307	HIBCH	cis	Thyroid	GTEx
rs760307	INPP1	cis	lymphoblastoid	seeQTL
rs760307	INPP1	cis	parietal	SCAN
rs760307	HIBCH	Cis_1M	lymphoblastoid	RTeQTL
rs760307	HIBCH	cis	parietal	SCAN
rs760307	HIBCH	cis	cerebellum	SCAN
rs760307	MFSD6	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191205800-191216200	Weak transcription	K562	blood
2	chr2:191207400-191208800	Active TSS	Primary T cells from cord blood	blood
3	chr2:191207400-191209200	Active TSS	Fetal Kidney	kidney
4	chr2:191207400-191209200	Active TSS	Osteobl	bone
5	chr2:191207400-191210000	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr2:191207600-191209200	Active TSS	Brain Anterior Caudate	brain
7	chr2:191207800-191209000	Active TSS	Fetal Brain Female	brain
8	chr2:191207800-191209200	Active TSS	Brain Hippocampus Middle	brain
9	chr2:191207800-191209200	Active TSS	Colon Smooth Muscle	Colon
10	chr2:191207800-191209400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr2:191207800-191209400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:191207800-191209400	Active TSS	A549	lung
13	chr2:191207800-191209600	Active TSS	HSMM	muscle
14	chr2:191208000-191209000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr2:191208000-191209000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:191208000-191209000	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr2:191208000-191209000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr2:191208000-191209000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:191208000-191209000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:191208000-191209000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr2:191208000-191209000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:191208000-191209000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:191208000-191209000	Active TSS	Adipose Nuclei	Adipose
24	chr2:191208000-191209000	Active TSS	Lung	lung
25	chr2:191208000-191209200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:191208000-191209200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:191208000-191209200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr2:191208000-191209200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:191208000-191209200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:191208000-191209200	Active TSS	Brain Substantia Nigra	brain
31	chr2:191208000-191209200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr2:191208000-191209200	Active TSS	Fetal Intestine Large	intestine
33	chr2:191208000-191209200	Active TSS	Gastric	stomach
34	chr2:191208000-191209400	Active TSS	Aorta	Aorta
35	chr2:191208000-191209400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:191208000-191209400	Active TSS	Colonic Mucosa	Colon
37	chr2:191208000-191209400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr2:191208000-191209400	Flanking Active TSS	HMEC	breast
39	chr2:191208000-191209600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:191208000-191209600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:191208000-191209600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr2:191208000-191209600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr2:191208000-191209600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:191208000-191209600	Active TSS	Ovary	ovary
45	chr2:191208000-191209600	Active TSS	Psoas Muscle	Psoas
46	chr2:191208000-191209600	Active TSS	HSMMtube	muscle
47	chr2:191208000-191209800	Active TSS	NH-A	brain
48	chr2:191208000-191210000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:191208000-191210600	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr2:191208200-191208800	Active TSS	Primary hematopoietic stem cells	blood

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