Variant report

Variant	rs1202834
Chromosome Location	chr1:58360111-58360112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:58358016..58360181-chr1:58361121..58362700,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1022636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202794	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1202797	0.96[ASN][1000 genomes]
rs1202798	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs1202799	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs1202800	0.96[ASN][1000 genomes]
rs1202801	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.96[ASN][1000 genomes]
rs1202804	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]
rs1202808	0.96[ASN][1000 genomes]
rs1202809	0.96[ASN][1000 genomes]
rs1202811	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]
rs1202828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1202829	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]
rs1202830	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202833	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1202835	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202836	0.81[EUR][1000 genomes]
rs1202837	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202839	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202840	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1202841	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1202842	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1202845	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1202846	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1202847	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1323833	0.82[YRI][hapmap]
rs1408143	0.82[YRI][hapmap]
rs1924267	0.82[YRI][hapmap]
rs2057225	1.00[JPT][hapmap]
rs2749274	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2749275	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2749276	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][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
rs1202834	PCSK9	cis	parietal	SCAN
rs1202834	C1orf87	cis	parietal	SCAN

Chromatin state (count:23 , 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	chr1:58358200-58360800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr1:58358400-58360800	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr1:58358400-58361000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:58358600-58360800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:58358600-58362000	Enhancers	HMEC	breast
7	chr1:58358800-58362000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:58359000-58360200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:58359400-58360800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:58359600-58360400	Enhancers	H9 Cell Line	embryonic stem cell
11	chr1:58359600-58360400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:58359600-58360800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:58359600-58361200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:58359600-58361200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:58359800-58360400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:58359800-58360400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:58359800-58361000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr1:58359800-58361200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:58359800-58361200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:58359800-58362000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:58359800-58362000	Enhancers	NHEK	skin
22	chr1:58360000-58360800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:58360000-58361000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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