Variant report

Variant	rs72666129
Chromosome Location	chr1:58324281-58324282
allele	G/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	USF1	chr1:58324267-58324760	H1-hESC	embryonic stem cell:	n/a	n/a
2	STAT3	chr1:58324011-58324403	MCF10A-Er-Src	breast:	n/a	chr1:58324023-58324031

Variant related genes	Relation type
DAB1-AS1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1408137	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17519798	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1886137	0.86[AMR][1000 genomes]
rs1886138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4912174	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4912284	0.86[AMR][1000 genomes]
rs4997596	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55733745	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55757801	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56016455	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56171994	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs68051884	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723714	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72664689	0.81[AMR][1000 genomes]
rs72666110	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72666111	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72666112	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72666114	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72666115	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72666118	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72666122	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72666124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72666127	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72666132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72666134	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72666135	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72666137	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72666141	0.85[AMR][1000 genomes];0.82[ASN][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	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv829937	chr1:58258288-58406506	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58320400-58325800	Weak transcription	Fetal Brain Female	brain
2	chr1:58320800-58330400	Weak transcription	Fetal Brain Male	brain
3	chr1:58321000-58325600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:58321000-58325800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:58321000-58326000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:58321200-58325800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:58322400-58327000	Enhancers	HMEC	breast
8	chr1:58322600-58325400	Enhancers	NHEK	skin
9	chr1:58322600-58327000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:58322800-58324800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:58323000-58324600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:58323200-58324400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:58323600-58325000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:58323800-58324600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:58323800-58325000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:58324000-58324400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:58324000-58324800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:58324000-58324800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr1:58324000-58324800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr1:58324000-58325400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:58324200-58324600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:58324200-58324600	Enhancers	Placenta	Placenta
23	chr1:58324200-58325000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:58324200-58325000	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links