Variant report

Variant	rs28549276
Chromosome Location	chr1:212872553-212872554
allele	C/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	CTCF	chr1:212872214-212873001	GM19238	blood:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
2	YY1	chr1:212872489-212872989	GM12878	blood:	n/a	n/a
3	TEAD4	chr1:212872482-212873026	H1-hESC	embryonic stem cell:	n/a	n/a
4	RUNX3	chr1:212872258-212872987	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:212872290-212874139	GM18505	blood:	n/a	n/a
6	SP1	chr1:212872442-212872850	A549	lung:	n/a	chr1:212872522-212872534 chr1:212872522-212872534 chr1:212872523-212872533 chr1:212872523-212872532
7	CTCF	chr1:212872144-212872964	H1-hESC	embryonic stem cell:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
8	USF2	chr1:212872425-212872883	H1-hESC	embryonic stem cell:	n/a	chr1:212872699-212872710
9	GABPA	chr1:212872519-212872978	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr1:212872283-212874137	GM12878	blood:	n/a	chr1:212873444-212873453
11	JUND	chr1:212872408-212873016	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr1:212872528-212872974	H1-hESC	embryonic stem cell:	n/a	n/a
13	EGR1	chr1:212872522-212872922	H1-hESC	embryonic stem cell:	n/a	chr1:212872599-212872609
14	BCLAF1	chr1:212872453-212872907	GM12878	blood:	n/a	n/a
15	BHLHE40	chr1:212872324-212874972	GM12878	blood:	n/a	chr1:212873287-212873303 chr1:212874387-212874396
16	BHLHE40	chr1:212872366-212873026	K562	blood:	n/a	n/a
17	MAX	chr1:212872288-212873571	K562	blood:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
18	USF1	chr1:212872508-212872842	SK-N-SH_RA	brain:	n/a	n/a
19	RAD21	chr1:212872256-212872959	H1-hESC	embryonic stem cell:	n/a	chr1:212872768-212872780 chr1:212872514-212872528 chr1:212872520-212872530
20	SMC3	chr1:212872503-212872890	K562	blood:	n/a	chr1:212872801-212872811 chr1:212872764-212872778 chr1:212872520-212872530 chr1:212872516-212872530
21	CTCF	chr1:212872460-212872610	GM12873	blood:	n/a	chr1:212872514-212872527 chr1:212872514-212872532 chr1:212872517-212872530
22	CTCF	chr1:212872537-212872883	NHEK	skin:	n/a	chr1:212872605-212872614 chr1:212872765-212872778 chr1:212872762-212872780
23	NANOG	chr1:212872518-212872929	H1-hESC	embryonic stem cell:	n/a	n/a
24	USF1	chr1:212872486-212872855	A549	lung:	n/a	n/a
25	CTCF	chr1:212872277-212872954	K562	blood:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
26	USF1	chr1:212872530-212872855	GM12878	blood:	n/a	n/a
27	CTCF	chr1:212872292-212872907	A549	lung:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
28	MAX	chr1:212872192-212873716	ECC-1	luminal epithelium:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
29	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
30	CTCF	chr1:212872120-212873181	K562	blood:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
31	RAD21	chr1:212872395-212872996	H1-hESC	embryonic stem cell:	n/a	chr1:212872768-212872780 chr1:212872514-212872528 chr1:212872520-212872530
32	NFIC	chr1:212872125-212872855	GM12878	blood:	n/a	n/a
33	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
34	TCF12	chr1:212872539-212872892	H1-hESC	embryonic stem cell:	n/a	n/a
35	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
36	CHD2	chr1:212872544-212873042	Hela-S3	cervix:	n/a	chr1:212872948-212872958
37	CTCF	chr1:212872361-212872939	A549	lung:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
38	TEAD4	chr1:212872552-212873050	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCFL	chr1:212872503-212872911	K562	blood:	n/a	chr1:212872769-212872778
40	MAX	chr1:212872526-212873389	Hela-S3	cervix:	n/a	chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212872699-212872714 chr1:212872700-212872710
41	MAX	chr1:212872227-212873605	HepG2	liver:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
42	CTCF	chr1:212872389-212872928	T-47D	breast:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
43	RAD21	chr1:212872207-212872953	HepG2	liver:	n/a	chr1:212872768-212872780 chr1:212872514-212872528 chr1:212872520-212872530
44	MAX	chr1:212872058-212873687	H1-hESC	embryonic stem cell:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
45	MYC	chr1:212872509-212872902	MCF10A-Er-Src	breast:	n/a	chr1:212872700-212872711 chr1:212872702-212872709 chr1:212872701-212872710 chr1:212872699-212872714 chr1:212872700-212872710
46	CCNT2	chr1:212872522-212873305	K562	blood:	n/a	chr1:212873224-212873233
47	JUND	chr1:212872355-212873113	A549	lung:	n/a	n/a
48	POLR2A	chr1:212872274-212874715	GM19193	blood:	n/a	n/a
49	REST	chr1:212872546-212872869	K562	blood:	n/a	chr1:212872596-212872609 chr1:212872594-212872604
50	CTBP2	chr1:212872308-212872868	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212779956..212785175-chr1:212870276..212874748,7	K562	blood:
2	chr1:212872476..212873206-chr1:213140873..213141422,2	K562	blood:
3	chr1:212872473..212873111-chr1:212955524..212956225,2	MCF-7	breast:
4	chr1:212779956..212783547-chr1:212870276..212874584,4	K562	blood:
5	chr1:212872500..212873127-chr1:212891520..212892244,2	MCF-7	breast:

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

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1156058	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3951343	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549091	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7549294	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9651103	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28549276	SNFT	Cis_1M	lymphoblastoid	RTeQTL
rs28549276	BATF3	cis	Whole Blood	GTEx
rs28549276	FLVCR1-AS1	cis	Whole Blood	GTEx
rs28549276	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs28549276	FLVCR1-AS1	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212870000-212872600	Flanking Active TSS	GM12878-XiMat	blood
2	chr1:212871800-212872600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
3	chr1:212871800-212872600	Enhancers	Small Intestine	intestine
4	chr1:212871800-212873000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
5	chr1:212871800-212873200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:212872000-212872600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr1:212872000-212872600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:212872000-212872600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:212872000-212872600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr1:212872000-212872600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:212872000-212872800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:212872000-212873000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr1:212872000-212873000	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr1:212872000-212873000	Bivalent Enhancer	Stomach Mucosa	stomach
15	chr1:212872000-212873000	Flanking Bivalent TSS/Enh	Thymus	Thymus
16	chr1:212872000-212873000	Flanking Bivalent TSS/Enh	NHEK	skin
17	chr1:212872000-212873800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr1:212872000-212874600	Active TSS	Brain Angular Gyrus	brain
19	chr1:212872000-212874800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:212872200-212872600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:212872200-212872600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:212872200-212872600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
23	chr1:212872200-212872600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr1:212872200-212872600	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr1:212872200-212872600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:212872200-212872600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr1:212872200-212872600	Flanking Active TSS	Aorta	Aorta
28	chr1:212872200-212872600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:212872200-212872600	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr1:212872200-212872600	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr1:212872200-212872600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
32	chr1:212872200-212872600	Flanking Active TSS	Gastric	stomach
33	chr1:212872200-212872600	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr1:212872200-212872600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
35	chr1:212872200-212872600	Flanking Bivalent TSS/Enh	Hela-S3	cervix
36	chr1:212872200-212872600	Flanking Bivalent TSS/Enh	K562	blood
37	chr1:212872200-212872600	Flanking Bivalent TSS/Enh	Osteobl	bone
38	chr1:212872200-212872800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:212872200-212872800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:212872200-212872800	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr1:212872200-212872800	Flanking Active TSS	Esophagus	oesophagus
42	chr1:212872200-212872800	Enhancers	Spleen	Spleen
43	chr1:212872200-212873000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr1:212872200-212873000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr1:212872200-212873000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:212872200-212873000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:212872200-212873000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain

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