Variant report

Variant	rs11875420
Chromosome Location	chr18:24357336-24357337
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 3 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11872394	0.91[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs7228785	0.96[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761995	chr18:24214286-24502570	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11875420	TTC39C	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:24351800-24360400	Weak transcription	Dnd41	blood
2	chr18:24355200-24358000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr18:24356600-24357400	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr18:24356600-24357800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr18:24356600-24357800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:24356600-24357800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr18:24356600-24357800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr18:24356600-24357800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr18:24356600-24358000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr18:24356600-24358200	Enhancers	Adipose Nuclei	Adipose
11	chr18:24356600-24359000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr18:24356600-24359000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr18:24356600-24361000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr18:24356800-24357400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr18:24356800-24358800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr18:24356800-24359200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr18:24357000-24357800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr18:24357000-24358000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr18:24357000-24358200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr18:24357200-24357600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr18:24357200-24357600	Enhancers	Fetal Muscle Trunk	muscle
22	chr18:24357200-24357600	Flanking Active TSS	Hela-S3	cervix
23	chr18:24357200-24357800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr18:24357200-24357800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr18:24357200-24357800	Enhancers	HMEC	breast
26	chr18:24357200-24358000	Enhancers	Fetal Muscle Leg	muscle
27	chr18:24357200-24358000	Enhancers	Fetal Stomach	stomach
28	chr18:24357200-24358000	Enhancers	NH-A	brain
29	chr18:24357200-24358200	Enhancers	H9 Cell Line	embryonic stem cell
30	chr18:24357200-24358200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr18:24357200-24358200	Enhancers	Fetal Kidney	kidney
32	chr18:24357200-24358600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr18:24357200-24359000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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