Variant report

Variant	rs2492779
Chromosome Location	chr1:212874024-212874025
allele	C/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	POLR2A	chr1:212872290-212874139	GM18505	blood:	n/a	n/a
2	MXI1	chr1:212872283-212874137	GM12878	blood:	n/a	chr1:212873444-212873453
3	BHLHE40	chr1:212872324-212874972	GM12878	blood:	n/a	chr1:212873287-212873303 chr1:212874387-212874396
4	BCL3	chr1:212873539-212874085	GM12878	blood:	n/a	chr1:212873916-212873925
5	E2F6	chr1:212872202-212874716	A549	lung:	n/a	chr1:212874470-212874477 chr1:212873219-212873229 chr1:212873421-212873431 chr1:212874470-212874477 chr1:212873224-212873233 chr1:212873180-212873190 chr1:212874470-212874477
6	ZNF263	chr1:212873482-212875668	HEK293-T-REx	kidney:	n/a	chr1:212874530-212874539 chr1:212874531-212874552
7	MYC	chr1:212871994-212874245	A549	lung:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
8	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
9	POLR2A	chr1:212873592-212874036	GM12878	blood:	n/a	n/a
10	STAT5A	chr1:212874019-212874528	GM12878	blood:	n/a	n/a
11	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
12	POLR2A	chr1:212872274-212874715	GM19193	blood:	n/a	n/a
13	BACH1	chr1:212872523-212874997	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:212872235-212874091	GM12892	blood:	n/a	n/a
15	MAX	chr1:212872184-212874186	K562	blood:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
16	GATA3	chr1:212873656-212874544	A549	lung:	n/a	chr1:212874075-212874092 chr1:212874236-212874245
17	POLR2A	chr1:212872353-212874121	GM18951	blood:	n/a	n/a
18	ZBTB7A	chr1:212873146-212874053	ECC-1	luminal epithelium:	n/a	n/a
19	NRF1	chr1:212873959-212874144	GM12878	blood:	n/a	n/a
20	MAX	chr1:212872350-212874359	GM12878	blood:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
21	RUNX3	chr1:212873195-212874897	GM12878	blood:	n/a	n/a
22	ELF1	chr1:212872170-212874347	GM12878	blood:	n/a	chr1:212873182-212873191
23	MAZ	chr1:212872379-212874090	GM12878	blood:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
24	EBF1	chr1:212873362-212874409	GM12878	blood:	n/a	chr1:212873685-212873698
25	ZNF143	chr1:212872125-212874164	GM12878	blood:	n/a	chr1:212873181-212873191 chr1:212873668-212873678 chr1:212872758-212872776
26	GATA2	chr1:212873601-212874979	SH-SY5Y	brain:	n/a	chr1:212874075-212874092 chr1:212874623-212874632 chr1:212874642-212874652 chr1:212874236-212874245
27	E2F6	chr1:212872502-212874630	A549	lung:	n/a	chr1:212874470-212874477 chr1:212873219-212873229 chr1:212873421-212873431 chr1:212874470-212874477 chr1:212873224-212873233 chr1:212873180-212873190 chr1:212874470-212874477
28	PML	chr1:212873235-212874599	GM12878	blood:	n/a	n/a
29	SUZ12	chr1:212873939-212874737	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr1:212872215-212874767	A549	lung:	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
31	SP1	chr1:212873898-212874524	A549	lung:	n/a	n/a
32	POLR2A	chr1:212872281-212874909	GM19099	blood:	n/a	n/a
33	POLR2A	chr1:212872378-212874705	GM18526	blood:	n/a	n/a
34	YY1	chr1:212873402-212874153	GM12878	blood:	n/a	chr1:212873555-212873566 chr1:212873421-212873435
35	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
36	YY1	chr1:212873496-212874196	GM12892	blood:	n/a	chr1:212873555-212873566
37	POLR2A	chr1:212872302-212874160	GM12878	blood:	n/a	n/a
38	CTBP2	chr1:212873561-212874574	H1-hESC	embryonic stem cell:	n/a	n/a
39	TBL1XR1	chr1:212873552-212874047	GM12878	blood:	n/a	n/a
40	CREB1	chr1:212873149-212874264	GM12878	blood:	n/a	n/a
41	RELA	chr1:212873395-212874108	GM15510	blood:	n/a	n/a
42	WRNIP1	chr1:212873952-212874199	GM12878	blood:	n/a	n/a
43	E2F6	chr1:212872277-212874157	K562	blood:	n/a	chr1:212873219-212873229 chr1:212873421-212873431 chr1:212873224-212873233 chr1:212873180-212873190
44	POLR2A	chr1:212872273-212874706	GM12892	blood:	n/a	n/a
45	MAZ	chr1:212872213-212874793	IMR90	lung:	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
46	NFIC	chr1:212873819-212874324	GM12878	blood:	n/a	n/a
47	MTA3	chr1:212872101-212874584	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:212872390-212874155	GM15510	blood:	n/a	n/a
49	RUNX3	chr1:212873923-212874486	GM12878	blood:	n/a	n/a
50	MXI1	chr1:212872149-212875007	IMR90	lung:	n/a	chr1:212873444-212873453

No.	Distal block	Cell Line	Cell type
1	chr1:212779956..212785175-chr1:212870276..212874748,7	K562	blood:
2	chr1:212780968..212782915-chr1:212872894..212874871,2	MCF-7	breast:
3	chr1:212873187..212876182-chr1:212968130..212971085,2	K562	blood:
4	chr1:212779956..212783547-chr1:212870276..212874584,4	K562	blood:

Variant related genes	Relation type
BATF3	TF binding region
ENSG00000203705	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1032965	0.83[AFR][1000 genomes]
rs1107215	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2246053	0.94[CHB][hapmap]
rs2456818	0.83[AFR][1000 genomes]
rs2456823	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2456827	0.83[AFR][1000 genomes]
rs2456828	0.83[AFR][1000 genomes]
rs2492784	0.83[AFR][1000 genomes]
rs2501860	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3003487	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738800	1.00[YRI][hapmap]
rs4951458	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv1829918	chr1:212828460-212874731	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2492779	FLVCR1-AS1	cis	lung	GTEx
rs2492779	SNFT	Cis_1M	lymphoblastoid	RTeQTL
rs2492779	FLVCR1-AS1	cis	Whole Blood	GTEx
rs2492779	SNFT	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212872000-212874600	Active TSS	Brain Angular Gyrus	brain
2	chr1:212872000-212874800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:212872200-212874600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:212872200-212874600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr1:212872200-212874600	Bivalent Enhancer	Fetal Brain Male	brain
6	chr1:212872200-212874600	Active TSS	A549	lung
7	chr1:212872200-212874800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr1:212872200-212874800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr1:212872200-212874800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr1:212872200-212874800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:212872400-212874200	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr1:212872400-212874200	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr1:212872400-212874200	Bivalent/Poised TSS	HSMM	muscle
14	chr1:212872400-212874400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:212872400-212874400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:212872400-212874600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:212872400-212874600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:212872400-212874600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:212872400-212874600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:212872400-212874600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:212872400-212874600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:212872400-212874600	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr1:212872400-212874600	Active TSS	Brain Cingulate Gyrus	brain
24	chr1:212872400-212874600	Active TSS	NHLF	lung
25	chr1:212872400-212874800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:212872400-212874800	Enhancers	Fetal Heart	heart
27	chr1:212872600-212874200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:212872600-212874200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr1:212872600-212874200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:212872600-212874400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr1:212872600-212874400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr1:212872600-212874400	Active TSS	Aorta	Aorta
33	chr1:212872600-212874600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:212872600-212874600	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr1:212872600-212874600	Active TSS	Colon Smooth Muscle	Colon
36	chr1:212872600-212874600	Active TSS	Rectal Smooth Muscle	rectum
37	chr1:212872600-212874600	Active TSS	Right Atrium	heart
38	chr1:212872600-212874600	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr1:212872600-212874600	Active TSS	Small Intestine	intestine
40	chr1:212872600-212874600	Active TSS	NHDF-Ad	bronchial
41	chr1:212872600-212874800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:212872600-212874800	Active TSS	Brain Substantia Nigra	brain
43	chr1:212872800-212874600	Bivalent/Poised TSS	Fetal Brain Female	brain
44	chr1:212872800-212874800	Active TSS	Brain Hippocampus Middle	brain
45	chr1:212872800-212874800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:212873000-212874200	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:212873000-212874400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
48	chr1:212873000-212874400	Active TSS	Ovary	ovary
49	chr1:212873000-212874400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
50	chr1:212873000-212874400	Bivalent/Poised TSS	Thymus	Thymus

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