Variant report

Variant	rs509237
Chromosome Location	chr5:112550247-112550248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11738528	0.81[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap]
rs1867324	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs2120349	0.83[MEX][hapmap]
rs2416309	0.86[ASW][hapmap];1.00[YRI][hapmap]
rs3846720	0.88[CHB][hapmap]
rs496977	1.00[YRI][hapmap]
rs637634	0.91[MEX][hapmap]
rs639680	1.00[YRI][hapmap]
rs680503	0.88[CHB][hapmap];0.87[MEX][hapmap]
rs6865129	0.88[CHB][hapmap];0.92[MEX][hapmap]
rs7717906	0.81[ASW][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs509237	TSSK1B	cis	cerebellum	SCAN
rs509237	YTHDC2	cis	cerebellum	SCAN
rs509237	NCRNA00219	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112539200-112554000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:112540800-112553400	Weak transcription	Brain Angular Gyrus	brain
3	chr5:112541800-112550400	Weak transcription	Esophagus	oesophagus
4	chr5:112542000-112553400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:112542000-112553400	Weak transcription	Lung	lung
6	chr5:112546600-112551800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr5:112546600-112555800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:112546800-112552800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:112546800-112553800	Enhancers	Ovary	ovary
10	chr5:112547000-112550600	Enhancers	Brain Substantia Nigra	brain
11	chr5:112547200-112551000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:112547200-112551800	Enhancers	Adipose Nuclei	Adipose
13	chr5:112547200-112553200	Enhancers	Fetal Heart	heart
14	chr5:112547200-112555600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:112547600-112551200	Enhancers	Brain Cingulate Gyrus	brain
16	chr5:112547800-112550600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:112547800-112550600	Enhancers	Fetal Muscle Leg	muscle
18	chr5:112547800-112551000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr5:112547800-112552400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:112547800-112555600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr5:112547800-112555800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr5:112548000-112550600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr5:112548000-112551000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:112548000-112551400	Enhancers	Left Ventricle	heart
25	chr5:112548000-112551400	Enhancers	Right Atrium	heart
26	chr5:112548000-112551400	Enhancers	Right Ventricle	heart
27	chr5:112548000-112552000	Enhancers	Placenta	Placenta
28	chr5:112548000-112552800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:112548000-112555600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr5:112548200-112552200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr5:112548200-112552200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:112548200-112552800	Enhancers	NHEK	skin
33	chr5:112548400-112551200	Weak transcription	NHDF-Ad	bronchial
34	chr5:112548400-112553200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:112548400-112581800	Weak transcription	Fetal Kidney	kidney
36	chr5:112548600-112551200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:112548600-112553400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:112548600-112554000	Weak transcription	HUVEC	blood vessel
39	chr5:112548800-112551400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:112548800-112551400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:112548800-112553200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:112549000-112554000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:112549200-112551400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:112549200-112551400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr5:112549400-112551600	Weak transcription	HMEC	breast
46	chr5:112549600-112550600	Enhancers	Brain Anterior Caudate	brain
47	chr5:112549600-112550800	Weak transcription	Brain Hippocampus Middle	brain
48	chr5:112549600-112559600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:112549800-112552800	Weak transcription	Liver	Liver
50	chr5:112550000-112550600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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