Variant report

Variant	rs558475
Chromosome Location	chr1:58601866-58601867
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11207173	0.95[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11207177	0.81[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs1213758	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1213759	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1213763	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1416342	0.81[EUR][1000 genomes]
rs2406590	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2797611	0.87[ASN][1000 genomes]
rs2806397	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4912302	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4912312	0.88[GIH][hapmap];0.81[TSI][hapmap]
rs515683	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs533114	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs581861	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs591970	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs602547	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs674913	0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs674986	0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs688010	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7529686	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7529800	0.91[ASN][1000 genomes]
rs7545320	0.88[GIH][hapmap];0.81[TSI][hapmap]
rs7550775	0.81[EUR][1000 genomes]
rs864250	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.95[ASN][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	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs558475	JUN	cis	parietal	SCAN
rs558475	DAB1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58599400-58607200	Weak transcription	Fetal Brain Female	brain
2	chr1:58600600-58602600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:58600600-58604200	Enhancers	Thymus	Thymus
4	chr1:58600800-58602200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr1:58600800-58602400	Enhancers	Primary T cells from cord blood	blood
6	chr1:58600800-58602600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:58601200-58602600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:58601400-58602400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:58601400-58602600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:58601400-58602600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:58601400-58602600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:58601600-58602400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:58601600-58602400	Enhancers	Primary hematopoietic stem cells	blood
14	chr1:58601600-58602400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:58601800-58602200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:58601800-58602200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:58601800-58602200	Flanking Active TSS	Fetal Thymus	thymus
18	chr1:58601800-58602400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:58601800-58602400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr1:58601800-58602400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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