Variant report

Variant	rs1372054
Chromosome Location	chr2:191208347-191208348
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	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	POLR2A	chr2:191208193-191208705	MCF-7	breast:	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	MAX	chr2:191207970-191209346	HepG2	liver:	n/a	chr2:191208347-191208356
12	PML	chr2:191207914-191209349	GM12878	blood:	n/a	n/a
13	FOXA2	chr2:191208218-191208658	A549	lung:	n/a	n/a
14	EGR1	chr2:191208076-191208522	GM12878	blood:	n/a	chr2:191208222-191208235
15	POLR2A	chr2:191207977-191208834	Hela-S3	cervix:	n/a	n/a
16	MAX	chr2:191208122-191209285	SK-N-SH	brain:	n/a	chr2:191208347-191208356
17	POLR2A	chr2:191208024-191209006	Hela-S3	cervix:	n/a	n/a
18	CHD2	chr2:191208285-191208686	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:191208024-191208996	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr2:191207854-191209161	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr2:191208012-191208889	HCT-116	colon:	n/a	n/a
22	FOS	chr2:191208006-191208612	HUVEC	blood vessel:	n/a	chr2:191208296-191208307
23	MAX	chr2:191207992-191209277	NB4	blood:	n/a	chr2:191208347-191208356
24	BHLHE40	chr2:191208274-191209297	HepG2	liver:	n/a	chr2:191208546-191208562 chr2:191208917-191208933
25	POLR2A	chr2:191208015-191209192	Hela-S3	cervix:	n/a	n/a
26	RCOR1	chr2:191207971-191208771	Hela-S3	cervix:	n/a	n/a
27	MBD4	chr2:191207883-191209386	HepG2	liver:	n/a	n/a
28	POLR2A	chr2:191208064-191208993	A549	lung:	n/a	n/a
29	MYC	chr2:191208173-191208894	MCF10A-Er-Src	breast:	n/a	chr2:191208347-191208356
30	MAX	chr2:191207959-191209312	A549	lung:	n/a	chr2:191208347-191208356
31	RFX5	chr2:191208217-191209747	Hela-S3	cervix:	n/a	n/a
32	FOSL2	chr2:191208062-191208754	HepG2	liver:	n/a	n/a
33	MXI1	chr2:191208194-191209291	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:191207896-191209102	Hela-S3	cervix:	n/a	n/a
35	MAX	chr2:191208298-191209208	HepG2	liver:	n/a	chr2:191208347-191208356
36	POLR2A	chr2:191208198-191209243	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:191208027-191208767	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr2:191208181-191208964	A549	lung:	n/a	n/a
39	MAX	chr2:191208025-191209245	Hela-S3	cervix:	n/a	chr2:191208347-191208356
40	HDAC2	chr2:191207946-191209314	HepG2	liver:	n/a	n/a
41	BRCA1	chr2:191208345-191208681	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:191208111-191208988	H1-neurons	neurons:	n/a	n/a
43	NFIC	chr2:191208154-191208954	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr2:191208174-191208810	A549	lung:	n/a	n/a
45	JUND	chr2:191208113-191208720	A549	lung:	n/a	n/a
46	BCLAF1	chr2:191208263-191208755	GM12878	blood:	n/a	chr2:191208546-191208559 chr2:191208425-191208434 chr2:191208554-191208567
47	POLR2A	chr2:191208008-191208477	PFSK-1	brain:	n/a	n/a
48	MAX	chr2:191207980-191209314	MCF-7	breast:	n/a	chr2:191208347-191208356
49	POLR2A	chr2:191208115-191208674	ECC-1	luminal epithelium:	n/a	n/a
50	E2F6	chr2:191207951-191209110	H1-hESC	embryonic stem cell:	n/a	chr2:191208994-191209006 chr2:191208413-191208420 chr2:191208413-191208420 chr2:191208413-191208420 chr2:191208425-191208435 chr2:191208599-191208608 chr2:191208547-191208557

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
ENSG00000151690	Chromatin interaction
ENSG00000198130	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1882892	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1984626	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2015744	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2016037	0.89[ASN][1000 genomes]
rs2067391	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067392	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2067393	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2067394	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067395	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2067397	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2067400	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2067402	0.87[ASN][1000 genomes]
rs2067405	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067406	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067407	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067408	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067409	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067412	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067414	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067415	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067416	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067417	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067420	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067421	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067423	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067424	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2067425	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2582753	0.88[ASN][1000 genomes]
rs2736621	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2736622	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3791815	0.87[ASN][1000 genomes]
rs3791816	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4656	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4853694	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6707602	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6707681	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721431	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72627906	0.87[ASN][1000 genomes]
rs972689	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs972690	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs972691	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs979329	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1372054	INPP1	Cis_1M	lymphoblastoid	RTeQTL
rs1372054	HIBCH	Cis_1M	lymphoblastoid	RTeQTL
rs1372054	HIBCH	cis	lung	GTEx
rs1372054	HIBCH	cis	Thyroid	GTEx

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	chr2:191207600-191208400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:191207600-191208400	Enhancers	Fetal Heart	heart
8	chr2:191207600-191208600	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr2:191207600-191209200	Active TSS	Brain Anterior Caudate	brain
10	chr2:191207800-191208400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr2:191207800-191209000	Active TSS	Fetal Brain Female	brain
12	chr2:191207800-191209200	Active TSS	Brain Hippocampus Middle	brain
13	chr2:191207800-191209200	Active TSS	Colon Smooth Muscle	Colon
14	chr2:191207800-191209400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr2:191207800-191209400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:191207800-191209400	Active TSS	A549	lung
17	chr2:191207800-191209600	Active TSS	HSMM	muscle
18	chr2:191208000-191208400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:191208000-191208400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:191208000-191208400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr2:191208000-191208400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr2:191208000-191208400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr2:191208000-191208400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:191208000-191208400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:191208000-191208400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:191208000-191208400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:191208000-191208400	Flanking Active TSS	Fetal Brain Male	brain
28	chr2:191208000-191208400	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr2:191208000-191208400	Flanking Active TSS	Thymus	Thymus
30	chr2:191208000-191208400	Flanking Active TSS	HepG2	liver
31	chr2:191208000-191208400	Flanking Active TSS	NHEK	skin
32	chr2:191208000-191208600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr2:191208000-191208600	Flanking Active TSS	GM12878-XiMat	blood
34	chr2:191208000-191209000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr2:191208000-191209000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:191208000-191209000	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr2:191208000-191209000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr2:191208000-191209000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:191208000-191209000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:191208000-191209000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr2:191208000-191209000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:191208000-191209000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:191208000-191209000	Active TSS	Adipose Nuclei	Adipose
44	chr2:191208000-191209000	Active TSS	Lung	lung
45	chr2:191208000-191209200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:191208000-191209200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:191208000-191209200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
48	chr2:191208000-191209200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:191208000-191209200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:191208000-191209200	Active TSS	Brain Substantia Nigra	brain

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