Variant report

Variant	rs1979368
Chromosome Location	chr18:9454478-9454479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9453398..9455231-chr18:9473452..9475581,2	MCF-7	breast:
2	chr18:9454174..9455775-chr18:9457951..9460126,2	K562	blood:
3	chr18:9403357..9405145-chr18:9454167..9455721,2	K562	blood:
4	chr18:9448423..9450289-chr18:9452565..9456767,3	K562	blood:
5	chr18:9448423..9451642-chr18:9452565..9457237,4	K562	blood:

Variant related genes	Relation type
ENSG00000017797	Chromatin interaction
ENSG00000273335	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12150769	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12960920	0.86[ASN][1000 genomes]
rs12968419	0.97[ASN][1000 genomes]
rs12968537	0.97[ASN][1000 genomes]
rs1462979	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1462980	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2864486	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2864487	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[ASN][1000 genomes]
rs2864488	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs35698222	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4325638	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4432308	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4798814	0.81[EUR][1000 genomes]
rs6506669	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506670	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506671	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7226449	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7228394	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7231518	0.83[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap]
rs7232382	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7235365	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7241396	0.97[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs8085051	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8091301	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs8096891	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9797471	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9951168	0.85[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	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1979368	C18orf1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9453600-9454800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:9453800-9454600	Enhancers	Fetal Brain Male	brain
3	chr18:9453800-9454800	Enhancers	K562	blood
4	chr18:9454000-9454600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr18:9454200-9454600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr18:9454200-9454600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:9454200-9454600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr18:9454200-9454600	Enhancers	Fetal Thymus	thymus
9	chr18:9454200-9454800	Enhancers	Fetal Heart	heart
10	chr18:9454400-9454800	Enhancers	HMEC	breast
11	chr18:9454400-9454800	Enhancers	NHEK	skin
12	chr18:9454400-9455600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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