Variant report

Variant	rs1202830
Chromosome Location	chr1:58357262-58357263
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1022636	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202798	0.92[ASN][1000 genomes]
rs1202799	0.92[ASN][1000 genomes]
rs1202828	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1202829	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1202833	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202834	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202835	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1202836	0.80[EUR][1000 genomes]
rs1202837	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202839	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1202840	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1202841	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1202842	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1202845	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1202846	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1202847	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2749274	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2749275	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2749276	0.95[AMR][1000 genomes];0.92[EUR][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	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
5	nsv1008205	chr1:58349005-58375261	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58347800-58359600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:58350600-58373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:58353600-58359800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:58354000-58358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:58354000-58358400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:58354200-58358200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:58354200-58358600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:58354400-58358200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:58354800-58359800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:58356000-58358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:58356000-58358400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:58356000-58358600	Weak transcription	HMEC	breast
13	chr1:58356000-58358600	Weak transcription	NHEK	skin
14	chr1:58356000-58359400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:58356200-58358400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:58356200-58359800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:58356400-58358400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:58356400-58360000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links