Variant report

Variant	rs17116869
Chromosome Location	chr1:58553974-58553975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10493244	0.93[CEU][hapmap]
rs10889083	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1106366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106367	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11207168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799299	0.93[CEU][hapmap]
rs11800351	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs11802821	0.91[CEU][hapmap]
rs12042276	0.81[CEU][hapmap]
rs12048970	0.91[CEU][hapmap]
rs12058945	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088082	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1213764	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1213770	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1213771	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1320555	0.83[CEU][hapmap]
rs13374932	0.91[CEU][hapmap]
rs1342875	0.91[CEU][hapmap]
rs1359494	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1359495	1.00[CEU][hapmap]
rs1416343	0.85[CEU][hapmap]
rs1416346	0.91[CEU][hapmap]
rs17116847	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs17116867	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17116983	0.91[CEU][hapmap]
rs17116988	0.91[CEU][hapmap]
rs17117013	0.91[CEU][hapmap]
rs17117039	0.93[CEU][hapmap]
rs17117101	0.91[CEU][hapmap]
rs17117119	0.85[CEU][hapmap]
rs1776184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1776192	0.92[CEU][hapmap]
rs1832488	0.91[CEU][hapmap]
rs1832489	0.91[CEU][hapmap]
rs1953811	0.91[CEU][hapmap]
rs1992481	0.83[CEU][hapmap]
rs2797608	0.91[CEU][hapmap]
rs2806405	0.95[JPT][hapmap]
rs3850534	0.81[CEU][hapmap]
rs3850535	0.91[CEU][hapmap]
rs3861823	0.83[CEU][hapmap]
rs3905539	0.91[CEU][hapmap]
rs4320799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58029039	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58745009	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59081310	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72906581	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74076064	0.83[EUR][1000 genomes]
rs7522031	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7551611	0.93[CEU][hapmap]
rs821525	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs821527	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs821528	0.86[CEU][hapmap]
rs821529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872691	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs873989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946310	0.83[CEU][hapmap]
rs9782935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58550400-58555400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:58550400-58555800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:58553400-58554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links