Variant report

Variant	rs4916258
Chromosome Location	chr1:172413526-172413527
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	GATA2	chr1:172412907-172413626	SH-SY5Y	brain:	n/a	n/a
2	TBP	chr1:172412775-172413594	K562	blood:	n/a	n/a
3	TAF7	chr1:172412975-172413564	H1-hESC	embryonic stem cell:	n/a	n/a
4	SMC3	chr1:172412739-172413529	Hela-S3	cervix:	n/a	chr1:172413288-172413302 chr1:172413291-172413301
5	POLR2A	chr1:172412769-172413529	SK-N-MC	brain:	n/a	n/a
6	CTCF	chr1:172412969-172413584	MCF-7	breast:	n/a	chr1:172413281-172413302 chr1:172413288-172413301 chr1:172413286-172413304
7	MAZ	chr1:172412671-172413555	K562	blood:	n/a	n/a
8	POLR2A	chr1:172412957-172413620	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr1:172412939-172413533	ECC-1	luminal epithelium:	n/a	n/a
10	GABPA	chr1:172412765-172413643	SK-N-SH	brain:	n/a	n/a
11	RCOR1	chr1:172412628-172413690	K562	blood:	n/a	n/a
12	TBP	chr1:172413060-172413680	HepG2	liver:	n/a	n/a
13	TAF1	chr1:172412971-172413622	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr1:172412782-172413570	A549	lung:	n/a	chr1:172413473-172413483
15	NFIC	chr1:172413037-172413605	ECC-1	luminal epithelium:	n/a	n/a
16	TCF12	chr1:172412713-172413615	A549	lung:	n/a	n/a
17	POLR2A	chr1:172412929-172413526	GM12878	blood:	n/a	n/a
18	RAD21	chr1:172412949-172413620	ECC-1	luminal epithelium:	n/a	chr1:172413287-172413300 chr1:172413284-172413303
19	SMC3	chr1:172413135-172413563	HepG2	liver:	n/a	chr1:172413288-172413302 chr1:172413291-172413301
20	RAD21	chr1:172413053-172413592	A549	lung:	n/a	chr1:172413287-172413300 chr1:172413284-172413303
21	MAX	chr1:172412664-172413609	A549	lung:	n/a	n/a
22	PAX5	chr1:172412984-172413639	GM12878	blood:	n/a	n/a
23	ELF1	chr1:172412696-172413725	HCT-116	colon:	n/a	n/a
24	CTCF	chr1:172412952-172413574	MCF-7	breast:	n/a	chr1:172413281-172413302 chr1:172413288-172413301 chr1:172413286-172413304
25	CTCF	chr1:172413074-172413535	K562	blood:	n/a	chr1:172413281-172413302 chr1:172413288-172413301 chr1:172413286-172413304
26	RAD21	chr1:172413082-172413568	IMR90	lung:	n/a	chr1:172413287-172413300 chr1:172413284-172413303
27	RCOR1	chr1:172412991-172413601	K562	blood:	n/a	n/a
28	MAX	chr1:172412949-172413560	MCF-7	breast:	n/a	n/a
29	MAX	chr1:172412960-172413673	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr1:172413085-172413654	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr1:172413004-172413548	GM12891	blood:	n/a	chr1:172413473-172413483
32	ELF1	chr1:172412708-172413541	GM12878	blood:	n/a	n/a
33	SP1	chr1:172412689-172413575	A549	lung:	n/a	chr1:172413445-172413459
34	POLR2A	chr1:172412686-172413671	GM19099	blood:	n/a	n/a
35	ELF1	chr1:172412762-172413548	K562	blood:	n/a	n/a
36	ELF1	chr1:172412764-172413606	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr1:172412046-172413557	MCF10A-Er-Src	breast:	n/a	n/a
38	GTF2F1	chr1:172412987-172413577	H1-hESC	embryonic stem cell:	n/a	n/a
39	TCF12	chr1:172412927-172413611	ECC-1	luminal epithelium:	n/a	n/a
40	USF2	chr1:172413094-172413545	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr1:172412280-172413895	A549	lung:	n/a	chr1:172413281-172413302 chr1:172413288-172413301 chr1:172413286-172413304
42	GABPA	chr1:172412781-172413609	HL-60	blood:	n/a	n/a
43	MAFF	chr1:172413232-172413578	HepG2	liver:	n/a	n/a
44	CTCF	chr1:172413048-172413549	H1-hESC	embryonic stem cell:	n/a	chr1:172413281-172413302 chr1:172413288-172413301 chr1:172413286-172413304
45	ZNF143	chr1:172413083-172413676	K562	blood:	n/a	n/a
46	YY1	chr1:172412990-172413648	H1-hESC	embryonic stem cell:	n/a	chr1:172413473-172413483
47	ELF1	chr1:172412772-172413549	A549	lung:	n/a	n/a
48	ZMIZ1	chr1:172413028-172413557	K562	blood:	n/a	n/a
49	POLR2A	chr1:172412940-172413654	HepG2	liver:	n/a	n/a
50	RAD21	chr1:172412839-172414010	SK-N-SH	brain:	n/a	chr1:172413287-172413300 chr1:172413284-172413303

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:172413492-172413542	PrEC	prostate:	n/a
2	chr1:172413492-172413542	HCF	heart:	n/a
3	chr1:172413492-172413542	SKMC	muscle:	n/a
4	chr1:172413492-172413542	AG04450	lung:	fetal
5	chr1:172413492-172413542	AG09309	skin:	n/a
6	chr1:172413492-172413542	SK-N-MC	brain:	n/a
7	chr1:172413492-172413542	HepG2	liver:	n/a
8	chr1:172413492-172413542	MCF-7	breast:	n/a
9	chr1:172413492-172413542	HPAEpiC	pulmonary alveolar:	n/a
10	chr1:172413492-172413542	HNPCEpiC	eye:	n/a
11	chr1:172413492-172413542	BE2_C	brain:	n/a
12	chr1:172413492-172413542	HMEC	breast:	n/a
13	chr1:172413492-172413542	ovcar-3	ovarian:	n/a
14	chr1:172413492-172413542	PANC-1	pancreas:	n/a
15	chr1:172413492-172413542	HCPEpiC	choroid plexus:	n/a
16	chr1:172413492-172413542	GM19239	blood:	n/a
17	chr1:172413492-172413542	AG09319	gingival:	n/a
18	chr1:172413492-172413542	HUVEC	blood vessel:	n/a
19	chr1:172413492-172413542	GM12878	blood:	n/a
20	chr1:172413492-172413542	NH-A	brain:	n/a
21	chr1:172413492-172413542	ProgFib	skin:	n/a
22	chr1:172413492-172413542	HRCEpiC	kidney:	n/a
23	chr1:172413492-172413542	BJ	skin:	n/a
24	chr1:172413492-172413542	NT2-D1	testis:	n/a
25	chr1:172413492-172413542	NHDF-neo	bronchial:	n/a
26	chr1:172413492-172413542	AoSMC	blood vessel:	n/a
27	chr1:172413492-172413542	GM12891	blood:	n/a
28	chr1:172413492-172413542	PFSK-1	brain:	n/a
29	chr1:172413492-172413542	Hela-S3	cervix:	n/a
30	chr1:172413492-172413542	HL-60	blood:	n/a
31	chr1:172413492-172413542	CMK	blood:	n/a
32	chr1:172413492-172413542	GM12892	blood:	n/a
33	chr1:172413492-172413542	HRE	kidney:	n/a
34	chr1:172413492-172413542	HCM	heart:	n/a
35	chr1:172413492-172413542	HEK293	kidney:	embryo
36	chr1:172413492-172413542	AG04449	skin:	fetal
37	chr1:172413492-172413542	NHBE	bronchial:	n/a
38	chr1:172413492-172413542	MCF10A-Er-Src	breast:	n/a
39	chr1:172413492-172413542	K562	blood:	n/a
40	chr1:172413492-172413542	SAEC	small airway:	n/a
41	chr1:172413492-172413542	HRPEpiC	eye:	n/a
42	chr1:172413492-172413542	U87	brain:	n/a
43	chr1:172413492-172413542	AG10803	skin:	n/a
44	chr1:172413492-172413542	Caco-2	colon:	n/a
45	chr1:172413492-172413542	SK-N-SH_RA	brain:	n/a
46	chr1:172413492-172413542	GM06990	blood:	n/a
47	chr1:172413492-172413542	IMR90	lung:	fetal
48	chr1:172413492-172413542	SK-N-SH	brain:	n/a
49	chr1:172413492-172413542	T-47D	breast:	n/a
50	chr1:172413492-172413542	ECC-1	luminal epithelium:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:172410326..172414934-chr1:172499314..172504781,7	K562	blood:
2	chr1:172411064..172415256-chr1:172501216..172504781,6	K562	blood:
3	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
4	chr1:172412087..172424934-chr1:172497120..172505334,59	MCF-7	breast:

Variant related genes	Relation type
PIGC	TF binding region
C1orf105	TF binding region
C1orf105	CpG island
PIGC	CpG island
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1063412	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10752946	0.81[ASN][1000 genomes]
rs10752957	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10798005	0.82[ASN][1000 genomes]
rs11484605	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13932	1.00[ASN][1000 genomes]
rs2269613	0.95[ASN][1000 genomes]
rs2269614	0.95[ASN][1000 genomes]
rs2269615	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269616	0.84[ASN][1000 genomes]
rs2285170	0.92[ASN][1000 genomes]
rs2285171	0.93[ASN][1000 genomes]
rs2285172	0.95[ASN][1000 genomes]
rs2285173	0.95[ASN][1000 genomes]
rs2285174	0.95[ASN][1000 genomes]
rs2285175	0.95[ASN][1000 genomes]
rs2285176	0.95[ASN][1000 genomes]
rs2301455	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2422141	0.85[ASN][1000 genomes]
rs3213563	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3937046	0.95[ASN][1000 genomes]
rs4916186	0.84[ASN][1000 genomes]
rs60302909	0.97[ASN][1000 genomes]
rs6424923	0.95[ASN][1000 genomes]
rs6658843	0.85[ASN][1000 genomes]
rs6673869	0.95[ASN][1000 genomes]
rs6674073	0.95[ASN][1000 genomes]
rs6689377	0.95[ASN][1000 genomes]
rs6702667	0.84[ASN][1000 genomes]
rs7411767	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7516301	0.81[ASN][1000 genomes]
rs929098	0.95[ASN][1000 genomes]
rs9425308	0.82[ASN][1000 genomes]
rs9425311	0.83[ASN][1000 genomes]
rs9425313	0.82[ASN][1000 genomes]
rs9425316	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425598	0.81[ASN][1000 genomes]
rs9425600	0.81[ASN][1000 genomes]
rs9425601	0.81[ASN][1000 genomes]
rs9425602	0.82[ASN][1000 genomes]
rs9425604	0.82[ASN][1000 genomes]
rs9425606	0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4916258	PIGC	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172411800-172413600	Active TSS	GM12878-XiMat	blood
2	chr1:172412000-172413600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:172412000-172413600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:172412000-172413600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:172412400-172413600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:172412400-172413600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:172412400-172413600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:172412400-172413600	Active TSS	Aorta	Aorta
9	chr1:172412400-172413600	Active TSS	Brain Hippocampus Middle	brain
10	chr1:172412400-172413600	Active TSS	Fetal Intestine Large	intestine
11	chr1:172412400-172413600	Active TSS	Ovary	ovary
12	chr1:172412400-172413600	Active TSS	A549	lung
13	chr1:172412400-172413800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:172412600-172413600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:172412600-172413600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr1:172412600-172413600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr1:172412600-172413600	Active TSS	HSMM	muscle
18	chr1:172412600-172413600	Active TSS	HSMMtube	muscle
19	chr1:172412600-172413800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:172412600-172413800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:172412600-172413800	Active TSS	Duodenum Mucosa	Duodenum
22	chr1:172412800-172413600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:172413000-172413600	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr1:172413200-172413600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr1:172413200-172413600	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr1:172413200-172413600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr1:172413200-172413600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:172413200-172413600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:172413200-172413600	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr1:172413200-172413600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr1:172413200-172413600	Enhancers	Fetal Heart	heart
32	chr1:172413200-172413600	Flanking Active TSS	Fetal Muscle Trunk	muscle
33	chr1:172413200-172413600	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr1:172413200-172413600	Flanking Active TSS	Placenta	Placenta
35	chr1:172413200-172413600	Flanking Active TSS	Fetal Thymus	thymus
36	chr1:172413200-172413600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr1:172413200-172413600	Enhancers	Stomach Mucosa	stomach
38	chr1:172413200-172413600	Enhancers	Spleen	Spleen
39	chr1:172413200-172413600	Flanking Active TSS	HUVEC	blood vessel
40	chr1:172413200-172413800	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr1:172413200-172413800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:172413200-172413800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr1:172413400-172413600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr1:172413400-172413600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
45	chr1:172413400-172413600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:172413400-172413600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:172413400-172413600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:172413400-172413600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
49	chr1:172413400-172413600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:172413400-172413600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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