Variant report

Variant	rs4945951
Chromosome Location	chr6:113780108-113780109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1033390	0.84[CHD][hapmap]
rs1033391	0.84[CHD][hapmap]
rs10484458	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12175106	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12214468	0.84[CHD][hapmap]
rs12526316	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12527509	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12528387	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1555030	0.80[ASN][1000 genomes]
rs1883170	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2049924	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2092088	0.80[ASN][1000 genomes]
rs2142638	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2142640	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2179114	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2179115	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2179116	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2179117	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294231	0.84[CHD][hapmap]
rs2348298	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2348299	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2348300	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2348301	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5001721	0.85[ASN][1000 genomes]
rs58748285	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6903255	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925126	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6928402	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724290	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs766330	0.85[ASN][1000 genomes]
rs7759869	0.84[CHD][hapmap]
rs7766686	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7776236	0.84[CHD][hapmap]
rs909542	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9320451	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9320452	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9320453	0.83[JPT][hapmap]
rs9320460	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9372363	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372364	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9374402	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9374403	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9374405	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9384867	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9384868	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9387146	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9387147	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9387149	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9398345	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9398346	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9398347	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9400626	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9400629	0.80[ASN][1000 genomes]
rs9400630	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9488196	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9488198	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9488199	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9488202	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[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	nsv916294	chr6:113518489-113904305	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1034256	chr6:113703567-113793790	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1021815	chr6:113703567-113799956	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1018357	chr6:113748468-113781070	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv518991	chr6:113760526-113799618	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4945951	GOPC	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113771600-113782400	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:113772400-113785800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr6:113777200-113785600	Weak transcription	A549	lung
4	chr6:113777800-113780600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:113778000-113780400	Enhancers	NH-A	brain
6	chr6:113778200-113780200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:113778200-113782400	Weak transcription	NHEK	skin
8	chr6:113778400-113780200	Enhancers	Fetal Lung	lung
9	chr6:113778400-113780400	Enhancers	Ovary	ovary
10	chr6:113779600-113780200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:113779800-113780200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:113779800-113780400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:113779800-113780400	Enhancers	HUVEC	blood vessel
14	chr6:113780000-113781800	Weak transcription	Placenta	Placenta
15	chr6:113780000-113781800	Weak transcription	NHDF-Ad	bronchial
16	chr6:113780000-113782000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:113780000-113782200	Weak transcription	Osteobl	bone
18	chr6:113780000-113782800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:113780000-113785400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:113780000-113785400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:113780000-113785400	Weak transcription	NHLF	lung

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