Variant report

Variant	rs2052661
Chromosome Location	chr18:11763020-11763021
allele	C/G
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	chr18:11761291..11763211-chr18:11764599..11766754,2	MCF-7	breast:
3	chr18:11760947..11763375-chr18:11800729..11802861,2	K562	blood:
4	chr18:11752451..11755153-chr18:11760955..11764568,3	K562	blood:
5	chr18:11752281..11755153-chr18:11760286..11763135,4	K562	blood:

Variant related genes	Relation type
ENSG00000141404	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11873821	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16976632	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs16976642	0.81[CHB][hapmap]
rs1895689	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2052660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28415243	0.84[ASN][1000 genomes]
rs28468616	0.95[AFR][1000 genomes]
rs2866279	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58518871	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6505671	0.94[ASN][1000 genomes]
rs6505674	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7227416	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7233178	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7240632	0.81[CEU][hapmap]
rs7359728	0.82[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8084370	0.82[AFR][1000 genomes]
rs8087001	0.87[ASN][1000 genomes]
rs8087789	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs8090320	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs8090628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][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];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8095592	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9947295	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs9949045	0.84[ASN][1000 genomes]
rs9951752	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9954406	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9957006	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9957311	0.82[AFR][1000 genomes];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

No data

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	chr18:11761200-11763200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr18:11761600-11765400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr18:11761600-11765600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr18:11761600-11766400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr18:11761600-11766800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr18:11761800-11763400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr18:11761800-11766000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:11761800-11767200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr18:11762200-11767000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr18:11762600-11765600	Weak transcription	H1 Cell Line	embryonic stem cell

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