Variant report

Variant	rs852788
Chromosome Location	chr1:58305551-58305552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10889075	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs1101354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207128	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs11582953	0.83[CEU][hapmap];0.88[JPT][hapmap]
rs11587998	0.90[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12117610	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs12402927	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs17519861	0.90[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17519924	0.90[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17579100	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17579464	0.88[JPT][hapmap]
rs1884486	0.91[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1936407	0.90[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2207986	0.90[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5014863	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57386386	0.80[ASN][1000 genomes]
rs61770276	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61770278	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61770279	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6670853	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs6679454	0.81[CEU][hapmap]
rs852759	0.90[JPT][hapmap]
rs852771	0.80[CHB][hapmap]
rs852789	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs852791	0.88[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs852799	0.90[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs852800	0.90[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58299200-58306000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:58301600-58306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:58301800-58306800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:58301800-58306800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:58304200-58305600	Enhancers	NH-A	brain
6	chr1:58304400-58306000	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr1:58304600-58305600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:58304600-58305800	Enhancers	Brain Germinal Matrix	brain

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