Variant report

Variant	rs852799
Chromosome Location	chr1:58321020-58321021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:58314989..58316769-chr1:58318311..58321122,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10889075	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1101354	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11207128	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes]
rs11582953	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11582988	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs11587998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12117610	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12402927	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17519861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17519924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17579100	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17579464	0.88[JPT][hapmap]
rs1884486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1936407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2207986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5014863	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57386386	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61770276	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61770278	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61770279	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670853	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6679454	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs6699475	0.84[CHB][hapmap]
rs852759	0.90[JPT][hapmap]
rs852788	0.90[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs852789	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs852790	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs852791	0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs852800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58315000-58322800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:58316000-58322600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:58318800-58321200	Enhancers	Fetal Lung	lung
4	chr1:58320400-58321200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:58320400-58325800	Weak transcription	Fetal Brain Female	brain
6	chr1:58320800-58330400	Weak transcription	Fetal Brain Male	brain
7	chr1:58321000-58325600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:58321000-58325800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:58321000-58326000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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