Variant report

Variant	rs443000
Chromosome Location	chr1:158656758-158656759
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	EP300	chr1:158655900-158656836	GM12878	blood:	n/a	n/a
2	IRF1	chr1:158655563-158657227	K562	blood:	n/a	chr1:158657050-158657060 chr1:158657049-158657063 chr1:158657049-158657061 chr1:158656597-158656611 chr1:158656599-158656610 chr1:158656598-158656612 chr1:158656598-158656608 chr1:158657050-158657064 chr1:158657050-158657061 chr1:158657048-158657061 chr1:158656598-158656609 chr1:158657048-158657061
3	ARID3A	chr1:158656270-158657331	K562	blood:	n/a	n/a
4	TBL1XR1	chr1:158655731-158657204	K562	blood:	n/a	n/a
5	POLR2A	chr1:158655573-158657125	PBDE	blood:	n/a	n/a
6	CEBPB	chr1:158656117-158657013	K562	blood:	n/a	n/a
7	CEBPD	chr1:158656224-158656767	K562	blood:	n/a	n/a
8	MAFF	chr1:158656296-158656839	K562	blood:	n/a	chr1:158656542-158656560
9	GATA1	chr1:158655836-158657462	PBDE	blood:	n/a	n/a
10	MAFK	chr1:158655841-158656761	K562	blood:	n/a	chr1:158656546-158656560 chr1:158656548-158656559 chr1:158656547-158656558 chr1:158656544-158656554 chr1:158656548-158656559 chr1:158656543-158656558 chr1:158656545-158656554 chr1:158656547-158656558
11	CEBPB	chr1:158656281-158656794	K562	blood:	n/a	n/a
12	EP300	chr1:158655784-158657475	K562	blood:	n/a	chr1:158657234-158657248
13	CUX1	chr1:158655832-158656814	K562	blood:	n/a	n/a
14	JUN	chr1:158656221-158656790	K562	blood:	n/a	chr1:158656543-158656553 chr1:158656573-158656585 chr1:158656543-158656553 chr1:158656544-158656552 chr1:158656543-158656553 chr1:158656542-158656554
15	BACH1	chr1:158655817-158657137	K562	blood:	n/a	n/a
16	IRF1	chr1:158654489-158657481	K562	blood:	n/a	chr1:158657050-158657060 chr1:158657049-158657063 chr1:158657049-158657061 chr1:158656597-158656611 chr1:158656599-158656610 chr1:158656598-158656612 chr1:158656598-158656608 chr1:158657050-158657064 chr1:158654494-158654506 chr1:158657050-158657061 chr1:158657048-158657061 chr1:158656598-158656609 chr1:158657048-158657061

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:158656718-158656768	Hepatocyte	liver:	n/a
2	chr1:158656718-158656768	K562	blood:	n/a
3	chr1:158656718-158656768	GM19239	blood:	n/a
4	chr1:158656718-158656768	A549	lung:	n/a
5	chr1:158656718-158656768	HIPEpiC	eye:	n/a
6	chr1:158656718-158656768	AG04450	lung:	fetal
7	chr1:158656718-158656768	SK-N-MC	brain:	n/a
8	chr1:158656718-158656768	HNPCEpiC	eye:	n/a
9	chr1:158656718-158656768	AG09309	skin:	n/a
10	chr1:158656718-158656768	GM12892	blood:	n/a
11	chr1:158656718-158656768	NH-A	brain:	n/a
12	chr1:158656718-158656768	HCT-116	colon:	n/a
13	chr1:158656718-158656768	PFSK-1	brain:	n/a
14	chr1:158656718-158656768	HPAEpiC	pulmonary alveolar:	n/a
15	chr1:158656718-158656768	Caco-2	colon:	n/a
16	chr1:158656718-158656768	ECC-1	luminal epithelium:	n/a
17	chr1:158656718-158656768	CMK	blood:	n/a
18	chr1:158656718-158656768	ProgFib	skin:	n/a
19	chr1:158656718-158656768	NT2-D1	testis:	n/a
20	chr1:158656718-158656768	AG10803	skin:	n/a
21	chr1:158656718-158656768	HUVEC	blood vessel:	n/a
22	chr1:158656718-158656768	HRE	kidney:	n/a
23	chr1:158656718-158656768	HMEC	breast:	n/a
24	chr1:158656718-158656768	U87	brain:	n/a
25	chr1:158656718-158656768	GM06990	blood:	n/a
26	chr1:158656718-158656768	BJ	skin:	n/a
27	chr1:158656718-158656768	NHDF-neo	bronchial:	n/a
28	chr1:158656718-158656768	GM12878	blood:	n/a
29	chr1:158656718-158656768	Hela-S3	cervix:	n/a
30	chr1:158656718-158656768	MCF-7	breast:	n/a
31	chr1:158656718-158656768	NB4	blood:	n/a
32	chr1:158656718-158656768	SK-N-SH_RA	brain:	n/a
33	chr1:158656718-158656768	BE2_C	brain:	n/a
34	chr1:158656718-158656768	NHBE	bronchial:	n/a
35	chr1:158656718-158656768	HL-60	blood:	n/a
36	chr1:158656718-158656768	HAEpiC	amniotic membrane:	n/a
37	chr1:158656718-158656768	LNCaP	prostate:	n/a
38	chr1:158656718-158656768	HCPEpiC	choroid plexus:	n/a
39	chr1:158656718-158656768	T-47D	breast:	n/a
40	chr1:158656718-158656768	HepG2	liver:	n/a
41	chr1:158656718-158656768	HEEpiC	esophagus:	n/a
42	chr1:158656718-158656768	AG09319	gingival:	n/a
43	chr1:158656718-158656768	HRCEpiC	kidney:	n/a
44	chr1:158656718-158656768	AoSMC	blood vessel:	n/a
45	chr1:158656718-158656768	PANC-1	pancreas:	n/a
46	chr1:158656718-158656768	HEK293	kidney:	embryo
47	chr1:158656718-158656768	HRPEpiC	eye:	n/a
48	chr1:158656718-158656768	ovcar-3	ovarian:	n/a
49	chr1:158656718-158656768	SAEC	small airway:	n/a
50	chr1:158656718-158656768	RPTEC	kidney:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158656464..158659384-chr1:159045094..159048407,3	K562	blood:

Variant related genes	Relation type
SPTA1	TF binding region
SPTA1	CpG island
ENSG00000163568	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11586270	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1652301	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1791672	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs188985	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs325993	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs378557	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs390718	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410483	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413190	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs413514	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs413543	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs431919	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs449694	0.82[ASN][1000 genomes]
rs451851	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs703115	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703116	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703121	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703122	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703123	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs703124	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703125	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703126	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs857923	0.82[ASN][1000 genomes]
rs857924	0.82[ASN][1000 genomes]
rs857929	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs857932	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs857933	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857934	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857936	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857937	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857941	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857942	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3491788	chr1:158537183-158725907	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3491789	chr1:158537242-158725858	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv872481	chr1:158625789-158712510	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv872482	chr1:158635852-158698532	Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv872483	chr1:158635852-158712510	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158655200-158657000	Active TSS	K562	blood
2	chr1:158655800-158657000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:158656000-158656800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:158656200-158656800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:158656200-158657000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr1:158656400-158657200	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links