Variant report

Variant	rs1202804
Chromosome Location	chr1:58376778-58376779
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1022636	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap];0.96[ASN][1000 genomes]
rs1202794	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1202797	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202798	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1202799	1.00[CEU][hapmap];0.88[CHB][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1202800	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202808	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202809	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202810	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1202811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202828	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1202829	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.81[MKK][hapmap]
rs1202833	0.96[ASN][1000 genomes]
rs1202834	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.87[MKK][hapmap];0.96[ASN][1000 genomes]
rs1202835	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.81[MKK][hapmap]
rs1202837	0.84[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.87[MKK][hapmap]
rs1202839	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs1202841	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs1202842	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1202846	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1202847	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2057225	0.86[JPT][hapmap]
rs2749274	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs2749275	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2749276	0.88[AFR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1202804	C1orf87	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58373800-58377400	Enhancers	Brain Germinal Matrix	brain
2	chr1:58375000-58376800	Weak transcription	Fetal Lung	lung
3	chr1:58375800-58377000	Enhancers	Left Ventricle	heart
4	chr1:58376200-58377000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:58376400-58377000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:58376400-58377000	Enhancers	HMEC	breast

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