Variant report

Variant	rs9990430
Chromosome Location	chr4:110964272-110964273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1557803	1.00[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs4141123	1.00[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs4698806	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs6533489	0.87[AMR][1000 genomes]
rs6837303	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][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	nsv869392	chr4:110945459-111235071	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9990430	CYP2U1	cis	parietal	SCAN
rs9990430	RRH	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110958000-110967400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:110962400-110964600	Enhancers	HepG2	liver
3	chr4:110962800-110964800	Enhancers	Fetal Kidney	kidney
4	chr4:110962800-110965400	Enhancers	Fetal Thymus	thymus
5	chr4:110963000-110964600	Enhancers	HSMM	muscle
6	chr4:110963000-110965400	Enhancers	Brain Germinal Matrix	brain
7	chr4:110963200-110964600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:110963200-110964600	Enhancers	Fetal Brain Male	brain
9	chr4:110963200-110965200	Enhancers	HSMMtube	muscle
10	chr4:110963400-110965000	Enhancers	Osteobl	bone
11	chr4:110963400-110965200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:110963400-110965400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:110963400-110972600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:110963400-110976200	Weak transcription	Fetal Intestine Large	intestine
15	chr4:110963600-110964400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:110963600-110964800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:110963600-110965000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:110963600-110965000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:110963600-110965400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:110963600-110967200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:110963600-110967600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:110963600-110967800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:110963600-110971000	Weak transcription	Liver	Liver
24	chr4:110963800-110964400	Weak transcription	Fetal Stomach	stomach
25	chr4:110963800-110964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:110963800-110974600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:110964000-110964400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:110964000-110964600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:110964000-110964600	Enhancers	Adipose Nuclei	Adipose
30	chr4:110964000-110964800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr4:110964000-110965000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:110964200-110964400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:110964200-110964400	Active TSS	Brain Anterior Caudate	brain
34	chr4:110964200-110964400	Flanking Active TSS	Dnd41	blood
35	chr4:110964200-110964600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:110964200-110964600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:110964200-110964600	Enhancers	Brain Angular Gyrus	brain
38	chr4:110964200-110964600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr4:110964200-110964600	Enhancers	Fetal Heart	heart
40	chr4:110964200-110964600	Enhancers	Fetal Lung	lung
41	chr4:110964200-110964600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr4:110964200-110964600	Enhancers	Stomach Smooth Muscle	stomach
43	chr4:110964200-110964600	Enhancers	NH-A	brain
44	chr4:110964200-110965000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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