Variant report

Variant	rs6699475
Chromosome Location	chr1:58371309-58371310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10889075	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11207128	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11582953	0.83[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11582988	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11587998	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12117610	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12141442	0.83[EUR][1000 genomes]
rs12402927	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17519861	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17519924	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17520463	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17579464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884486	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs1936407	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2207986	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs57060206	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58020116	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770282	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61770283	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6670853	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6679454	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs852799	0.84[CHB][hapmap]
rs852800	0.86[CHB][hapmap]

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:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58350600-58373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:58362000-58376400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:58363600-58374200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:58364600-58372200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:58367600-58372200	Weak transcription	Fetal Brain Male	brain
6	chr1:58368200-58373600	Weak transcription	Fetal Brain Female	brain
7	chr1:58371200-58372200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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