Variant report

Variant	rs2973049
Chromosome Location	chr5:37818139-37818140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1862574	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs2910702	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs2910708	0.98[ASN][1000 genomes]
rs2910712	0.86[ASN][1000 genomes]
rs2910713	0.87[ASN][1000 genomes]
rs2973048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973050	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973051	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][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	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2973049	UGT3A2	cis	cerebellum	SCAN
rs2973049	DHX33	trans	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37811200-37818200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:37812200-37822200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:37813400-37824400	Weak transcription	Fetal Kidney	kidney
4	chr5:37815000-37822200	Weak transcription	Fetal Intestine Small	intestine
5	chr5:37815800-37830600	Weak transcription	Ovary	ovary
6	chr5:37816000-37818200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:37816200-37834000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:37816400-37822000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:37816600-37818200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr5:37816600-37818200	Enhancers	Brain Substantia Nigra	brain
11	chr5:37816600-37818400	Enhancers	Rectal Smooth Muscle	rectum
12	chr5:37816800-37823000	Weak transcription	NHEK	skin
13	chr5:37816800-37830600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:37816800-37831600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:37817000-37821800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:37817000-37831800	Weak transcription	NH-A	brain
17	chr5:37817200-37825400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:37817400-37818800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:37817400-37820000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:37817400-37823200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:37817400-37823400	Weak transcription	HSMM	muscle
22	chr5:37817400-37824000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:37817400-37824000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:37817400-37826800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:37817400-37831800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:37817600-37818400	Genic enhancers	Fetal Stomach	stomach
27	chr5:37817600-37818800	Weak transcription	HSMMtube	muscle
28	chr5:37817600-37819600	Strong transcription	NHDF-Ad	bronchial
29	chr5:37817800-37818200	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr5:37817800-37818400	Strong transcription	Stomach Smooth Muscle	stomach
31	chr5:37817800-37819600	Enhancers	Colon Smooth Muscle	Colon
32	chr5:37817800-37824200	Strong transcription	Osteobl	bone
33	chr5:37818000-37818200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:37818000-37818400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:37818000-37819400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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