Variant report

Variant	rs12038999
Chromosome Location	chr1:75807380-75807381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1004053	0.85[ASN][1000 genomes]
rs10493571	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10493573	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874149	0.85[ASN][1000 genomes]
rs11163074	0.83[ASN][1000 genomes]
rs11163089	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163095	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11163154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163155	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163185	0.89[ASN][1000 genomes]
rs1249655	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1249656	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249657	0.89[ASN][1000 genomes]
rs1249659	0.89[ASN][1000 genomes]
rs1249660	0.89[ASN][1000 genomes]
rs1249670	0.85[ASN][1000 genomes]
rs1249675	0.85[ASN][1000 genomes]
rs12562924	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726507	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12744088	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12756704	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343517	0.88[ASN][1000 genomes]
rs1505258	0.89[ASN][1000 genomes]
rs1613680	0.89[ASN][1000 genomes]
rs1700893	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2135142	0.89[ASN][1000 genomes]
rs2657206	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593571	0.85[ASN][1000 genomes]
rs6658610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548993	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013952	chr1:75716654-75936048	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv535004	chr1:75716654-75936048	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75803600-75807800	Enhancers	Primary B cells from peripheral blood	blood
2	chr1:75804800-75807600	Enhancers	GM12878-XiMat	blood
3	chr1:75805000-75808200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:75805000-75808200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:75805200-75807600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:75805200-75808000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:75805200-75808000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:75805800-75807400	Enhancers	Fetal Brain Male	brain
9	chr1:75806400-75807800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:75807000-75809200	Enhancers	Brain Germinal Matrix	brain
11	chr1:75807000-75812400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:75807200-75807400	Enhancers	Fetal Brain Female	brain
13	chr1:75807200-75808200	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links