Variant report

Variant	rs6918374
Chromosome Location	chr6:53867005-53867006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10080737	0.85[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10948796	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17554427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273892	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62396327	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900464	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6906625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748750	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7761919	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764823	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296733	0.85[CEU][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes]
rs9367549	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9474699	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9474700	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9474701	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1018062	chr6:53842588-53925192	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6918374	C6orf142	cis	cerebellum	SCAN
rs6918374	MLIP-IT1	cis	Esophagus Mucosa	GTEx
rs6918374	ELOVL5	cis	cerebellum	SCAN
rs6918374	PRIM2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53852400-53867800	Weak transcription	Fetal Heart	heart
2	chr6:53861000-53867200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:53862000-53870000	Weak transcription	Aorta	Aorta
4	chr6:53864000-53867800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:53864200-53867200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:53864200-53867800	Weak transcription	Adipose Nuclei	Adipose
7	chr6:53864400-53874400	Weak transcription	Psoas Muscle	Psoas
8	chr6:53864400-53875000	Weak transcription	Left Ventricle	heart
9	chr6:53865200-53873200	Weak transcription	Liver	Liver
10	chr6:53865800-53868000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:53866200-53868400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:53866200-53869200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:53866400-53867600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:53866400-53869000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:53866600-53867600	Enhancers	Osteobl	bone
16	chr6:53866600-53868600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:53866600-53869000	Enhancers	NHEK	skin
18	chr6:53866800-53867400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:53866800-53867400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr6:53866800-53868600	Enhancers	HMEC	breast
21	chr6:53867000-53868800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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