Variant report

Variant	rs1320555
Chromosome Location	chr1:58561954-58561955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1004297	0.84[ASN][1000 genomes]
rs10493244	0.91[CEU][hapmap]
rs10889083	0.98[ASN][1000 genomes]
rs10889084	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1106366	0.83[CEU][hapmap]
rs1106367	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11207168	0.83[CEU][hapmap]
rs11207169	0.83[CEU][hapmap]
rs11207170	0.83[CEU][hapmap]
rs11799299	0.91[CEU][hapmap]
rs11802821	0.91[CEU][hapmap]
rs12031853	0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs12048970	0.91[CEU][hapmap]
rs12058945	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1213764	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1213770	0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs1213771	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs13374932	0.91[CEU][hapmap]
rs1342875	0.91[CEU][hapmap];0.84[MEX][hapmap]
rs1359495	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1416343	0.83[CEU][hapmap]
rs1416346	0.91[CEU][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs17116847	0.83[CEU][hapmap]
rs17116867	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17116869	0.83[CEU][hapmap]
rs17116983	0.91[CEU][hapmap]
rs17116988	0.91[CEU][hapmap]
rs17117013	0.91[CEU][hapmap]
rs17117039	0.91[CEU][hapmap]
rs17117101	0.91[CEU][hapmap]
rs17117119	0.83[CEU][hapmap]
rs1776184	0.83[CEU][hapmap]
rs1776192	0.91[CEU][hapmap]
rs1832488	0.89[CEU][hapmap]
rs1832489	0.91[CEU][hapmap]
rs1953811	0.91[CEU][hapmap]
rs1992481	0.83[CEU][hapmap]
rs2406589	0.83[ASN][1000 genomes]
rs2764682	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2764685	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2764686	0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2764687	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs2797608	0.91[CEU][hapmap]
rs2806406	0.81[CHB][hapmap]
rs3118212	0.84[ASN][1000 genomes]
rs3121907	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs3850535	0.91[CEU][hapmap]
rs3861823	0.83[CEU][hapmap]
rs3905539	0.91[CEU][hapmap]
rs4320799	0.83[CEU][hapmap]
rs57918745	0.83[ASN][1000 genomes]
rs58029039	0.99[ASN][1000 genomes]
rs59081310	0.99[ASN][1000 genomes]
rs74076064	0.87[ASN][1000 genomes]
rs7522031	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7551611	0.91[CEU][hapmap]
rs821525	0.99[ASN][1000 genomes]
rs821526	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821527	0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs821528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821529	0.83[CEU][hapmap]
rs873989	0.83[CEU][hapmap]
rs946310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9782935	0.83[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1320555	DAB1	cis	cerebellum	SCAN
rs1320555	PCSK9	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58555800-58563400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:58557200-58563400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:58557400-58562200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:58557400-58563400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:58557400-58563400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:58557400-58563600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:58557400-58563600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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