Variant report

Variant	rs2113739
Chromosome Location	chr18:11761954-11761955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:11751544..11753668-chr18:11760267..11763186,2	MCF-7	breast:
2	chr18:11755901..11758017-chr18:11761238..11762763,2	MCF-7	breast:
3	chr18:11761291..11763211-chr18:11764599..11766754,2	MCF-7	breast:
4	chr18:11760947..11763375-chr18:11800729..11802861,2	K562	blood:
5	chr18:11752451..11755153-chr18:11760955..11764568,3	K562	blood:
6	chr18:11752281..11755153-chr18:11760286..11763135,4	K562	blood:

Variant related genes	Relation type
ENSG00000141404	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11873821	0.94[ASN][1000 genomes]
rs16976632	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs16976642	0.81[CHB][hapmap]
rs1895689	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2052660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28415243	0.84[ASN][1000 genomes]
rs2866279	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs58518871	0.94[ASN][1000 genomes]
rs6505671	0.94[ASN][1000 genomes]
rs6505674	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7227416	0.81[ASN][1000 genomes]
rs7233178	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7240632	0.80[CEU][hapmap]
rs7359728	0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs8087001	0.87[ASN][1000 genomes]
rs8087789	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap]
rs8090320	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs8090628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8095592	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9949045	0.84[ASN][1000 genomes]
rs9951752	0.85[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9954406	0.94[ASN][1000 genomes]
rs9957006	0.94[ASN][1000 genomes]
rs9957311	0.94[ASN][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	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1065382	chr18:11723230-11769732	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv833590	chr18:11757329-11924539	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2113739	C18orf1	cis	parietal	SCAN
rs2113739	RHOH	trans	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11752800-11767200	Weak transcription	Aorta	Aorta
2	chr18:11752800-11774000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:11753000-11767200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr18:11753000-11767200	Weak transcription	Esophagus	oesophagus
5	chr18:11753000-11768000	Weak transcription	HMEC	breast
6	chr18:11753000-11774800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr18:11753000-11775400	Weak transcription	Gastric	stomach
8	chr18:11754000-11765400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr18:11755000-11765400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr18:11755200-11765600	Weak transcription	Brain Germinal Matrix	brain
11	chr18:11756600-11769200	Weak transcription	Fetal Brain Female	brain
12	chr18:11758200-11766800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr18:11758400-11785600	Weak transcription	Brain Anterior Caudate	brain
14	chr18:11760000-11765000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr18:11760800-11762200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr18:11761000-11762600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr18:11761200-11763200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr18:11761600-11765400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr18:11761600-11765600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr18:11761600-11766400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr18:11761600-11766800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr18:11761800-11763400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr18:11761800-11766000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:11761800-11767200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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