Variant report

Variant	rs7731209
Chromosome Location	chr5:37816845-37816846
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]
rs11951867	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs16903732	0.88[MEX][hapmap]
rs17386472	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs62360372	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7721618	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.84[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	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
rs7731209	AGXT2	cis	cerebellum	SCAN
rs7731209	LIFR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37811200-37817200	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:37811200-37818200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:37812200-37822200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:37812800-37817200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:37813400-37824400	Weak transcription	Fetal Kidney	kidney
6	chr5:37814000-37817000	Enhancers	HMEC	breast
7	chr5:37815000-37817000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:37815000-37822200	Weak transcription	Fetal Intestine Small	intestine
9	chr5:37815800-37817400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:37815800-37817400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr5:37815800-37830600	Weak transcription	Ovary	ovary
12	chr5:37816000-37817200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr5:37816000-37817800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:37816000-37818200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:37816200-37817000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:37816200-37817200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:37816200-37817200	Weak transcription	Fetal Stomach	stomach
18	chr5:37816200-37817200	Genic enhancers	HSMMtube	muscle
19	chr5:37816200-37817400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr5:37816200-37817400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:37816200-37817400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:37816200-37817600	Genic enhancers	NHDF-Ad	bronchial
23	chr5:37816200-37817800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:37816200-37818000	Enhancers	Brain Hippocampus Middle	brain
25	chr5:37816200-37834000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:37816400-37817000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:37816400-37817000	Enhancers	Brain Angular Gyrus	brain
28	chr5:37816400-37817200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr5:37816400-37817400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr5:37816400-37817400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr5:37816400-37817400	Enhancers	HSMM	muscle
32	chr5:37816400-37817800	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:37816400-37817800	Genic enhancers	Osteobl	bone
34	chr5:37816400-37818000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:37816400-37822000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:37816600-37817000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:37816600-37817000	Enhancers	NH-A	brain
38	chr5:37816600-37817400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:37816600-37817400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:37816600-37817400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr5:37816600-37817600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:37816600-37817600	Enhancers	Brain Cingulate Gyrus	brain
43	chr5:37816600-37818200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr5:37816600-37818200	Enhancers	Brain Substantia Nigra	brain
45	chr5:37816600-37818400	Enhancers	Rectal Smooth Muscle	rectum
46	chr5:37816800-37817000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:37816800-37817400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:37816800-37823000	Weak transcription	NHEK	skin
49	chr5:37816800-37830600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:37816800-37831600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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