Variant report

Variant	rs12133990
Chromosome Location	chr1:93428105-93428106
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	POU2F2	chr1:93428055-93428419	GM12891	blood:	n/a	chr1:93428222-93428244 chr1:93428228-93428237 chr1:93428229-93428237 chr1:93428224-93428242 chr1:93428225-93428238 chr1:93428223-93428244
2	POLR2A	chr1:93425826-93428558	GM12878	blood:	n/a	n/a
3	POU2F2	chr1:93427911-93428492	GM12891	blood:	n/a	chr1:93428222-93428244 chr1:93428228-93428237 chr1:93428229-93428237 chr1:93428224-93428242 chr1:93428225-93428238 chr1:93428223-93428244
4	POLR2A	chr1:93425974-93428432	GM18526	blood:	n/a	n/a
5	POLR2A	chr1:93427836-93428337	GM12878	blood:	n/a	n/a
6	SRF	chr1:93427721-93428392	HCT-116	colon:	n/a	chr1:93427991-93428006 chr1:93427993-93428004 chr1:93427992-93428005 chr1:93427988-93428006 chr1:93427994-93428003 chr1:93427992-93428005 chr1:93427990-93428007 chr1:93427994-93428005 chr1:93427990-93428008
7	ATF2	chr1:93427940-93428423	H1-hESC	embryonic stem cell:	n/a	n/a
8	PML	chr1:93425555-93428546	GM12878	blood:	n/a	n/a
9	YY1	chr1:93427807-93428436	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZNF384	chr1:93427562-93428441	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:93427850-93428281	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr1:93428063-93428287	MCF10A-Er-Src	breast:	n/a	chr1:93428231-93428240
13	STAT1	chr1:93427929-93428270	GM12878	blood:	n/a	chr1:93428178-93428201
14	FOS	chr1:93427999-93428365	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr1:93428101-93428301	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr1:93425647-93428513	IMR90	lung:	n/a	chr1:93427313-93427323 chr1:93428231-93428240
17	SRF	chr1:93427794-93428259	MCF-7	breast:	n/a	chr1:93427991-93428006 chr1:93427993-93428004 chr1:93427992-93428005 chr1:93427988-93428006 chr1:93427994-93428003 chr1:93427992-93428005 chr1:93427990-93428007 chr1:93427994-93428005 chr1:93427990-93428008
18	YY1	chr1:93426851-93428492	GM12878	blood:	n/a	chr1:93427316-93427330 chr1:93427195-93427206 chr1:93427198-93427212 chr1:93426874-93426885 chr1:93427115-93427129 chr1:93427400-93427414 chr1:93427331-93427342 chr1:93427437-93427451 chr1:93427260-93427269
19	RELA	chr1:93427698-93428469	GM12878	blood:	n/a	n/a
20	SRF	chr1:93427757-93428251	ECC-1	luminal epithelium:	n/a	chr1:93427991-93428006 chr1:93427993-93428004 chr1:93427992-93428005 chr1:93427988-93428006 chr1:93427994-93428003 chr1:93427992-93428005 chr1:93427990-93428007 chr1:93427994-93428005 chr1:93427990-93428008
21	BATF	chr1:93428055-93428375	GM12878	blood:	n/a	chr1:93428209-93428220
22	POLR2A	chr1:93427750-93428236	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr1:93426795-93428377	MCF10A-Er-Src	breast:	n/a	n/a
24	ZMIZ1	chr1:93427183-93428110	K562	blood:	n/a	n/a
25	JUND	chr1:93428074-93428198	H1-hESC	embryonic stem cell:	n/a	n/a
26	ATF2	chr1:93427523-93428492	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:93426739-93428372	ProgFib	skin:	n/a	n/a
28	MAX	chr1:93427836-93428150	K562	blood:	n/a	n/a
29	MYC	chr1:93427808-93428322	MCF10A-Er-Src	breast:	n/a	chr1:93428231-93428240
30	CHD1	chr1:93427154-93428515	GM12878	blood:	n/a	n/a
31	RELA	chr1:93425928-93428479	GM15510	blood:	n/a	chr1:93426541-93426550 chr1:93426541-93426550
32	ZNF384	chr1:93427789-93428304	K562	blood:	n/a	n/a
33	SRF	chr1:93427592-93428422	HCT-116	colon:	n/a	chr1:93427991-93428006 chr1:93427993-93428004 chr1:93427992-93428005 chr1:93427988-93428006 chr1:93427994-93428003 chr1:93427992-93428005 chr1:93427990-93428007 chr1:93427994-93428005 chr1:93427990-93428008
34	NFATC1	chr1:93427827-93428522	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:93425557-93428497	GM18505	blood:	n/a	n/a
36	POLR2A	chr1:93427787-93428531	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:93425643-93429210	GM12891	blood:	n/a	n/a
38	RELA	chr1:93425735-93428545	GM12891	blood:	n/a	chr1:93426541-93426550 chr1:93426541-93426550
39	POLR2A	chr1:93425948-93428399	GM19193	blood:	n/a	n/a
40	POLR2A	chr1:93425928-93428432	GM12878	blood:	n/a	n/a
41	JUND	chr1:93427874-93428373	H1-hESC	embryonic stem cell:	n/a	chr1:93428207-93428218
42	TAF7	chr1:93427702-93428123	H1-hESC	embryonic stem cell:	n/a	n/a
43	ZEB1	chr1:93428059-93428434	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:93428091-93428323	H1-hESC	embryonic stem cell:	n/a	n/a
45	POU2F2	chr1:93428061-93428376	GM12878	blood:	n/a	chr1:93428222-93428244 chr1:93428228-93428237 chr1:93428229-93428237 chr1:93428224-93428242 chr1:93428225-93428238 chr1:93428223-93428244
46	YY1	chr1:93427829-93428295	GM12878	blood:	n/a	n/a
47	PML	chr1:93427896-93428346	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:93425948-93428384	GM12892	blood:	n/a	n/a
49	PAX5	chr1:93427930-93428443	GM12878	blood:	n/a	n/a
50	STAT3	chr1:93428066-93428272	MCF10A-Er-Src	breast:	n/a	chr1:93428178-93428201

No.	Distal block	Cell Line	Cell type
1	chr1:93425993..93428373-chr1:93433568..93436256,2	MCF-7	breast:
2	chr1:93427351..93429788-chr1:93458702..93460989,2	MCF-7	breast:
3	chr1:93296356..93298770-chr1:93426282..93429088,3	MCF-7	breast:
4	chr1:93324499..93325053-chr1:93427932..93428772,2	MCF-7	breast:
5	chr1:93323615..93326108-chr1:93427081..93429012,3	K562	blood:
6	chr1:93425058..93429733-chr1:93431759..93435608,8	K562	blood:
7	chr1:93323615..93326108-chr1:93427081..93429012,2	K562	blood:

Variant related genes	Relation type
FAM69A	TF binding region
ENSG00000122406	Chromatin interaction
ENSG00000252121	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1011663	0.85[ASN][1000 genomes]
rs10747454	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164850	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164851	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164854	0.90[ASN][1000 genomes]
rs12049007	0.85[ASN][1000 genomes]
rs12120036	0.85[ASN][1000 genomes]
rs12130044	0.85[ASN][1000 genomes]
rs12144226	0.95[ASN][1000 genomes]
rs1415069	0.86[ASN][1000 genomes]
rs2086314	0.85[ASN][1000 genomes]
rs2127398	0.85[ASN][1000 genomes]
rs2127400	0.85[ASN][1000 genomes]
rs28561471	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3943283	0.85[ASN][1000 genomes]
rs4515797	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4847226	0.84[ASN][1000 genomes]
rs4847389	0.80[ASN][1000 genomes]
rs514235	0.85[ASN][1000 genomes]
rs534409	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs663112	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6671078	0.83[ASN][1000 genomes]
rs6671268	0.85[ASN][1000 genomes]
rs6681429	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7517539	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7524934	0.87[ASN][1000 genomes]
rs770883	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs945630	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	esv3339713	chr1:93425789-93428737	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12133990	FAM69A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93425200-93428200	Active TSS	Liver	Liver
2	chr1:93425200-93428200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr1:93425200-93428200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:93425200-93428200	Active TSS	Brain Substantia Nigra	brain
5	chr1:93425400-93428200	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:93425400-93428200	Active TSS	Brain Angular Gyrus	brain
7	chr1:93425400-93428200	Active TSS	Brain Anterior Caudate	brain
8	chr1:93425600-93428200	Active TSS	Colonic Mucosa	Colon
9	chr1:93425600-93428200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:93425600-93428400	Active TSS	Aorta	Aorta
11	chr1:93425800-93428200	Active TSS	GM12878-XiMat	blood
12	chr1:93426000-93428200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:93426000-93428200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:93426000-93428200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr1:93426000-93428200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:93426000-93428200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:93426000-93428200	Active TSS	Fetal Kidney	kidney
18	chr1:93426000-93428200	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr1:93426000-93428200	Active TSS	Stomach Smooth Muscle	stomach
20	chr1:93426000-93428200	Active TSS	HepG2	liver
21	chr1:93426000-93428200	Active TSS	HSMMtube	muscle
22	chr1:93426000-93428400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:93426400-93428200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:93426400-93428200	Active TSS	H1 Cell Line	embryonic stem cell
25	chr1:93426400-93428200	Active TSS	Duodenum Mucosa	Duodenum
26	chr1:93426600-93428200	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr1:93426600-93428200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:93427400-93428200	Flanking Active TSS	Fetal Thymus	thymus
29	chr1:93427400-93428200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr1:93427400-93428400	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr1:93427400-93428400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:93427400-93428400	Flanking Active TSS	Dnd41	blood
33	chr1:93427600-93428200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:93427600-93428200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr1:93427600-93428200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr1:93427600-93428200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr1:93427600-93428200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:93427600-93428200	Flanking Active TSS	NH-A	brain
39	chr1:93427600-93428200	Flanking Active TSS	NHEK	skin
40	chr1:93427600-93428400	Flanking Active TSS	K562	blood
41	chr1:93427800-93428200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr1:93427800-93428200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:93427800-93428200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr1:93427800-93428200	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr1:93427800-93428200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:93427800-93428200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:93427800-93428200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr1:93427800-93428200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:93427800-93428200	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr1:93427800-93428200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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