Variant report

Variant	rs873989
Chromosome Location	chr1:58556598-58556599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10493244	0.91[CEU][hapmap]
rs10889083	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1106366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106367	1.00[CEU][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11207168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799299	0.91[CEU][hapmap]
rs11800351	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11802821	0.91[CEU][hapmap]
rs12048970	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs12058945	1.00[CEU][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088082	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1213764	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1213770	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1213771	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1320555	0.83[CEU][hapmap]
rs13374932	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs1342875	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs1359494	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1359495	1.00[CEU][hapmap]
rs1416343	0.81[CEU][hapmap]
rs1416346	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs17116847	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs17116867	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17116869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116983	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs17116988	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs17117013	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs17117039	0.91[CEU][hapmap]
rs17117101	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs17117119	0.81[CEU][hapmap]
rs1776184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1776192	0.90[CEU][hapmap]
rs1832488	0.88[CEU][hapmap]
rs1832489	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs1953811	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs1992481	0.81[CEU][hapmap]
rs2797608	0.90[CEU][hapmap]
rs2806405	0.95[JPT][hapmap]
rs3850535	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs3861823	0.81[CEU][hapmap]
rs3905539	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs4320799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58029039	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58745009	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59081310	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72906581	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74076064	0.83[EUR][1000 genomes]
rs7522031	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7551611	0.91[CEU][hapmap]
rs821525	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs821527	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs821528	0.83[CEU][hapmap]
rs821529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872691	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946310	0.83[CEU][hapmap]
rs9782935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs873989	PCSK9	cis	parietal	SCAN
rs873989	TTC4	cis	cerebellum	SCAN
rs873989	HSPB11	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58554200-58557400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr1:58554800-58556600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:58554800-58557400	Enhancers	Fetal Brain Male	brain
4	chr1:58555000-58556600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:58555200-58556800	Enhancers	Fetal Lung	lung
6	chr1:58555400-58557400	Enhancers	Brain Germinal Matrix	brain
7	chr1:58555600-58557200	Enhancers	Fetal Brain Female	brain
8	chr1:58555600-58557400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:58555800-58556600	Enhancers	Primary T cells from cord blood	blood
10	chr1:58555800-58557400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:58555800-58557400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr1:58555800-58563400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:58556000-58557000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:58556000-58557400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr1:58556000-58557400	Enhancers	Fetal Kidney	kidney
16	chr1:58556200-58556600	Bivalent Enhancer	Fetal Thymus	thymus
17	chr1:58556200-58557000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr1:58556400-58556800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:58556400-58556800	Bivalent Enhancer	Thymus	Thymus
20	chr1:58556400-58557200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:58556400-58557400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:58556400-58557400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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