Variant report

Variant	rs3003487
Chromosome Location	chr1:212874932-212874933
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	CEBPB	chr1:212874665-212875744	Hela-S3	cervix:	n/a	chr1:212875631-212875644
2	BHLHE40	chr1:212872324-212874972	GM12878	blood:	n/a	chr1:212873287-212873303 chr1:212874387-212874396
3	TCF7L2	chr1:212874589-212875733	Hela-S3	cervix:	n/a	n/a
4	ZNF263	chr1:212873482-212875668	HEK293-T-REx	kidney:	n/a	chr1:212874530-212874539 chr1:212874531-212874552
5	MAX	chr1:212872207-212875186	NB4	blood:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212874385-212874396 chr1:212872701-212872710 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873443-212873451 chr1:212874394-212874404 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
6	MYC	chr1:212873185-212875195	NB4	blood:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212873225-212873235 chr1:212874385-212874396 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873443-212873451 chr1:212874394-212874404 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212873444-212873455 chr1:212873445-212873454
7	CEBPB	chr1:212874480-212875511	A549	lung:	n/a	n/a
8	CTCF	chr1:212874820-212874970	HVMF	connective:	n/a	n/a
9	BACH1	chr1:212872523-212874997	H1-hESC	embryonic stem cell:	n/a	n/a
10	EBF1	chr1:212874889-212875199	GM12878	blood:	n/a	chr1:212875005-212875016 chr1:212875034-212875043 chr1:212875032-212875045 chr1:212875032-212875043 chr1:212875033-212875043 chr1:212875034-212875043
11	KAP1	chr1:212874486-212875731	U2OS	brain:	n/a	n/a
12	EBF1	chr1:212874897-212875139	GM12878	blood:	n/a	chr1:212875005-212875016 chr1:212875034-212875043 chr1:212875032-212875045 chr1:212875032-212875043 chr1:212875033-212875043 chr1:212875034-212875043
13	POLR2A	chr1:212874537-212875401	K562	blood:	n/a	n/a
14	GATA2	chr1:212873601-212874979	SH-SY5Y	brain:	n/a	chr1:212874075-212874092 chr1:212874623-212874632 chr1:212874642-212874652 chr1:212874236-212874245
15	GATA2	chr1:212874314-212875067	HUVEC	blood vessel:	n/a	chr1:212874623-212874632 chr1:212874642-212874652
16	EBF1	chr1:212873372-212875258	GM12878	blood:	n/a	chr1:212875005-212875016 chr1:212875034-212875043 chr1:212875032-212875045 chr1:212875032-212875043 chr1:212873685-212873698 chr1:212875033-212875043 chr1:212875034-212875043
17	RCOR1	chr1:212874732-212874958	Hela-S3	cervix:	n/a	n/a
18	KAP1	chr1:212874328-212875675	HEK293	kidney:	n/a	n/a
19	FOXA2	chr1:212874721-212874971	HepG2	liver:	n/a	n/a
20	MXI1	chr1:212872149-212875007	IMR90	lung:	n/a	chr1:212873444-212873453
21	CTCF	chr1:212874820-212874970	NHDF-neo	bronchial:	n/a	n/a
22	TCF7L2	chr1:212874397-212875835	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212873187..212876182-chr1:212968130..212971085,2	K562	blood:

Variant related genes	Relation type
BATF3	TF binding region
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1107215	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2246053	0.81[ASN][1000 genomes]
rs2456823	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2492779	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501860	0.94[EUR][1000 genomes];0.96[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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3003487	FLVCR1-AS1	cis	lung	GTEx
rs3003487	FLVCR1-AS1	cis	Whole Blood	GTEx
rs3003487	SNFT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212874200-212875200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr1:212874200-212875200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:212874200-212875200	Enhancers	Placenta	Placenta
4	chr1:212874400-212875000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
5	chr1:212874400-212875000	Enhancers	Liver	Liver
6	chr1:212874400-212875000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:212874400-212875000	Bivalent Enhancer	Fetal Intestine Small	intestine
8	chr1:212874400-212875200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:212874400-212875800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr1:212874600-212875000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
11	chr1:212874600-212875000	Enhancers	Aorta	Aorta
12	chr1:212874600-212875000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr1:212874600-212875000	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr1:212874600-212875000	Flanking Bivalent TSS/Enh	A549	lung
15	chr1:212874600-212875200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
16	chr1:212874600-212875200	Enhancers	Primary B cells from peripheral blood	blood
17	chr1:212874600-212875200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr1:212874600-212875200	Bivalent Enhancer	Fetal Intestine Large	intestine
19	chr1:212874600-212875400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:212874600-212875400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:212874600-212876400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:212874800-212875000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
23	chr1:212874800-212875000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr1:212874800-212875000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
25	chr1:212874800-212875000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:212874800-212875000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
27	chr1:212874800-212875000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr1:212874800-212875000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr1:212874800-212875000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:212874800-212875000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:212874800-212875000	Enhancers	Adipose Nuclei	Adipose
32	chr1:212874800-212875000	Enhancers	Brain Angular Gyrus	brain
33	chr1:212874800-212875000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr1:212874800-212875000	Enhancers	Colon Smooth Muscle	Colon
35	chr1:212874800-212875000	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr1:212874800-212875000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
37	chr1:212874800-212875000	Bivalent Enhancer	GM12878-XiMat	blood
38	chr1:212874800-212875000	Bivalent Enhancer	HepG2	liver
39	chr1:212874800-212875000	Bivalent Enhancer	NH-A	brain
40	chr1:212874800-212875000	Bivalent Enhancer	Osteobl	bone
41	chr1:212874800-212875200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:212874800-212875200	Bivalent Enhancer	Stomach Mucosa	stomach
43	chr1:212874800-212875200	Bivalent Enhancer	Hela-S3	cervix
44	chr1:212874800-212875200	Bivalent Enhancer	NHDF-Ad	bronchial
45	chr1:212874800-212875200	Enhancers	NHLF	lung
46	chr1:212874800-212876400	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:212874800-212877200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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