Variant report

Variant	rs9940273
Chromosome Location	chr16:65090541-65090542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13331791	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1520235	0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28378738	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7202828	0.83[AMR][1000 genomes]
rs9922115	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs9923368	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs9937744	0.83[AMR][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	nsv948640	chr16:64859061-65112790	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv833260	chr16:65050647-65218759	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1831	chr16:65071976-65106105	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9940273	FXYD2	trans	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:65058600-65104400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:65069800-65105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr16:65072800-65096200	Weak transcription	Colon Smooth Muscle	Colon
4	chr16:65074400-65094000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:65079000-65093000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr16:65080200-65091000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:65081800-65094800	Weak transcription	Lung	lung
8	chr16:65082800-65093200	Strong transcription	NH-A	brain
9	chr16:65083800-65100000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr16:65085000-65095800	Weak transcription	Fetal Brain Female	brain
11	chr16:65087400-65104800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr16:65087800-65091000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr16:65087800-65100600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr16:65087800-65102000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr16:65087800-65103600	Weak transcription	Aorta	Aorta
16	chr16:65088000-65091200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr16:65088000-65093800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr16:65088000-65095600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr16:65088200-65091000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr16:65088200-65093200	Enhancers	Brain Anterior Caudate	brain
21	chr16:65088200-65101600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr16:65088400-65091000	Weak transcription	Fetal Kidney	kidney
23	chr16:65088400-65093600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr16:65088600-65093400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr16:65088800-65093400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr16:65089000-65091000	Weak transcription	Spleen	Spleen
27	chr16:65089000-65093200	Strong transcription	Osteobl	bone
28	chr16:65089200-65090600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr16:65089200-65091200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr16:65089200-65091600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr16:65089200-65093000	Enhancers	Brain Substantia Nigra	brain
32	chr16:65089400-65091200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr16:65089400-65098000	Weak transcription	Fetal Muscle Leg	muscle
34	chr16:65089400-65101200	Weak transcription	Fetal Brain Male	brain
35	chr16:65089600-65091000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr16:65089600-65092000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:65089600-65092200	Weak transcription	Brain Angular Gyrus	brain
38	chr16:65089600-65095600	Weak transcription	HSMMtube	muscle
39	chr16:65089800-65090800	Strong transcription	NHDF-Ad	bronchial
40	chr16:65090000-65090600	Strong transcription	Fetal Stomach	stomach
41	chr16:65090000-65092000	Genic enhancers	Ovary	ovary
42	chr16:65090400-65090600	Enhancers	HMEC	breast
43	chr16:65090400-65090600	Weak transcription	HSMM	muscle
44	chr16:65090400-65090800	Weak transcription	Brain Hippocampus Middle	brain
45	chr16:65090400-65091800	Strong transcription	NHLF	lung
46	chr16:65090400-65092200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr16:65090400-65093400	Strong transcription	Fetal Lung	lung
48	chr16:65090400-65099800	Enhancers	Brain Cingulate Gyrus	brain

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