Variant report

Variant	rs11265519
Chromosome Location	chr1:160878913-160878914
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160874204..160876595-chr1:160877694..160880011,2	MCF-7	breast:
2	chr1:160872347..160875327-chr1:160877154..160879416,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10797087	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10908809	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10908810	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10908811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908812	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908813	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11265510	0.96[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11265514	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11265516	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11587040	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12080285	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12125065	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12126310	0.82[JPT][hapmap];0.90[MEX][hapmap]
rs12135639	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12740520	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1810924	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1855186	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1855187	0.84[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1930596	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1930598	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2039415	0.88[CEU][hapmap];0.95[MEX][hapmap];0.87[EUR][1000 genomes]
rs2184064	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2225591	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2236515	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2274905	0.84[CEU][hapmap]
rs2274907	0.84[CEU][hapmap]
rs2274908	0.84[CEU][hapmap]
rs2274910	0.84[CEU][hapmap]
rs2297559	0.87[EUR][1000 genomes]
rs34295669	0.82[EUR][1000 genomes]
rs3766356	0.84[CEU][hapmap]
rs3818724	0.85[EUR][1000 genomes]
rs3820094	0.84[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs3829790	0.85[MEX][hapmap]
rs3953093	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3953095	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4017453	0.82[EUR][1000 genomes]
rs4129196	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656277	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4656282	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4656956	0.84[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs4656957	0.84[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs4656958	0.88[CEU][hapmap];0.95[MEX][hapmap];0.87[EUR][1000 genomes]
rs4656959	0.95[EUR][1000 genomes]
rs4656964	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4656971	0.85[MEX][hapmap]
rs6427552	0.84[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6427553	0.86[EUR][1000 genomes]
rs6658416	0.86[EUR][1000 genomes]
rs6671490	0.82[EUR][1000 genomes]
rs6691868	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6694415	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6704490	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7411035	0.84[ASW][hapmap];0.88[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.86[EUR][1000 genomes]
rs7414826	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7516660	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs7551697	0.93[EUR][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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv3430322	chr1:160851829-160920480	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv947200	chr1:160870136-160905390	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11265519	C4orf11	trans	multi-tissue	Pritchard
rs11265519	SPTA1	cis	parietal	SCAN
rs11265519	LMNA	cis	parietal	SCAN
rs11265519	APCS	cis	cerebellum	SCAN
rs11265519	SLAMF8	cis	multi-tissue	Pritchard
rs11265519	AF009262	trans	multi-tissue	Pritchard
rs11265519	XM_065434	trans	multi-tissue	Pritchard
rs11265519	NDUFS2	cis	cerebellum	SCAN
rs11265519	RP11-312J18.6	cis	Thyroid	GTEx
rs11265519	OR5B21	cis	Liver	GTEx
rs11265519	LY9	cis	Liver	GTEx
rs11265519	LY9	trans	multi-tissue	Pritchard
rs11265519	IGSF4B	cis	multi-tissue	Pritchard
rs11265519	SEMA5A	cis	Liver	GTEx
rs11265519	OR5B21	trans	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160875400-160880600	Weak transcription	Fetal Intestine Small	intestine
2	chr1:160875600-160880600	Weak transcription	Pancreas	Pancrea
3	chr1:160875800-160879200	Enhancers	Fetal Heart	heart
4	chr1:160875800-160879800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:160875800-160880600	Weak transcription	Right Ventricle	heart
6	chr1:160876600-160881200	Weak transcription	Stomach Mucosa	stomach
7	chr1:160877800-160880200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:160878400-160879200	Enhancers	Right Atrium	heart
9	chr1:160878400-160880000	Enhancers	Gastric	stomach
10	chr1:160878400-160880000	Enhancers	Left Ventricle	heart
11	chr1:160878600-160879000	Weak transcription	Ovary	ovary

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