Variant report

Variant	rs1202799
Chromosome Location	chr1:58374090-58374091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1022636	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs1202794	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1202797	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1202798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202800	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202801	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202804	1.00[CEU][hapmap];0.88[CHB][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1202808	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1202809	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1202810	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1202811	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1202828	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs1202829	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1202830	0.92[ASN][1000 genomes]
rs1202834	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs1202835	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1202837	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs1202839	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1202840	0.81[ASN][1000 genomes]
rs1202841	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1202845	0.92[ASN][1000 genomes]
rs1202846	0.91[AFR][1000 genomes]
rs1202847	0.91[AFR][1000 genomes]
rs2749274	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2749275	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2749276	0.91[AFR][1000 genomes]

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:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58362000-58376400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:58363600-58374200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:58372200-58376600	Enhancers	Fetal Brain Male	brain
4	chr1:58373200-58375000	Enhancers	Fetal Lung	lung
5	chr1:58373600-58376200	Enhancers	Fetal Brain Female	brain
6	chr1:58373800-58374600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:58373800-58374600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:58373800-58377400	Enhancers	Brain Germinal Matrix	brain
9	chr1:58374000-58374400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:58374000-58374600	Enhancers	Cortex derived primary cultured neurospheres	brain

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