Variant report

Variant	rs12360876
Chromosome Location	chr11:5389950-5389951
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10837945	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11037097	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1473547	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs1532514	0.90[JPT][hapmap]
rs2340327	0.94[JPT][hapmap]
rs2471983	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2471984	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2647545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2647547	0.95[JPT][hapmap]
rs2647548	0.95[JPT][hapmap]
rs2647550	0.95[JPT][hapmap]
rs2647551	0.95[JPT][hapmap]
rs2647552	0.95[JPT][hapmap]
rs2647555	0.95[JPT][hapmap]
rs2647556	0.95[JPT][hapmap]
rs2647611	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2723375	0.95[JPT][hapmap]
rs2736537	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2736538	0.95[JPT][hapmap]
rs2736539	0.95[JPT][hapmap]
rs2736540	0.95[JPT][hapmap]
rs2736541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2736544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2736546	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2736549	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2736551	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4301813	0.87[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4494328	0.90[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6421052	0.83[JPT][hapmap]
rs7479727	0.94[JPT][hapmap]
rs951747	0.94[JPT][hapmap]
rs9734220	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524400	chr11:5328361-5416622	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
3	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv896931	chr11:5357881-5505149	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv832057	chr11:5375585-5576200	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv983147	chr11:5376861-5392760	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12360876	HBE1	cis	parietal	SCAN
rs12360876	DNHD1	cis	parietal	SCAN
rs12360876	ART1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5384200-5391200	Enhancers	NHLF	lung
2	chr11:5384200-5391200	Enhancers	Osteobl	bone
3	chr11:5385000-5391400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:5386000-5391200	Enhancers	NHDF-Ad	bronchial
5	chr11:5388000-5390200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr11:5388000-5390400	Enhancers	Hela-S3	cervix
7	chr11:5388200-5390400	Enhancers	HSMM	muscle
8	chr11:5389000-5390600	Weak transcription	HSMMtube	muscle
9	chr11:5389400-5390400	Enhancers	K562	blood
10	chr11:5389400-5391200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr11:5389600-5390400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr11:5389600-5390600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:5389600-5390800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:5389800-5390000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr11:5389800-5390200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr11:5389800-5391200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr11:5389800-5391200	Enhancers	HUES64 Cell Line	embryonic stem cell

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