Variant report

Variant	rs1202829
Chromosome Location	chr1:58355969-58355970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1022636	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202794	0.94[CEU][hapmap];0.88[CHB][hapmap]
rs1202798	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1202799	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1202801	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.93[MKK][hapmap]
rs1202804	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.81[MKK][hapmap]
rs1202810	0.88[ASN][1000 genomes]
rs1202811	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.81[MKK][hapmap]
rs1202828	1.00[CEU][hapmap];0.88[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1202830	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1202833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202834	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202835	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202836	0.80[EUR][1000 genomes]
rs1202837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1202839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1202840	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1202841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1202842	0.93[CEU][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1202845	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1202846	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1202847	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1323833	0.82[YRI][hapmap]
rs1408143	0.82[YRI][hapmap]
rs1924267	0.82[YRI][hapmap]
rs2749274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2749275	0.94[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2749276	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7544285	0.82[YRI][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1202829	PCSK9	cis	parietal	SCAN
rs1202829	C1orf87	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58347800-58359600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:58350600-58373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:58353600-58359800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:58354000-58358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:58354000-58358400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:58354200-58358200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:58354200-58358600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:58354400-58358200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:58354800-58356000	Enhancers	NH-A	brain
10	chr1:58354800-58359800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:58355000-58356200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:58355200-58356000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:58355200-58356000	Enhancers	HMEC	breast
14	chr1:58355400-58356400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:58355600-58356000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:58355600-58356000	Enhancers	NHEK	skin
17	chr1:58355600-58356200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:58355800-58356000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:58355800-58356000	Enhancers	HUES6 Cell Line	embryonic stem cell

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