Variant report

Variant	rs12659754
Chromosome Location	chr5:112535345-112535346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10070231	0.87[EUR][1000 genomes]
rs11241196	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11738528	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12332686	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12656003	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1822489	0.80[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867324	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3846720	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs680503	0.88[CHB][hapmap];0.84[MEX][hapmap]
rs6865129	0.80[CEU][hapmap];0.88[CHB][hapmap];0.80[MEX][hapmap]
rs6899208	0.94[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12659754	YTHDC2	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112515800-112538000	Weak transcription	Fetal Kidney	kidney
2	chr5:112518600-112538600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112522000-112538800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:112522600-112541000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:112527400-112538800	Weak transcription	Esophagus	oesophagus
6	chr5:112528600-112538600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:112529000-112538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:112530200-112538800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:112530600-112536400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:112531200-112535400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:112531400-112538600	Weak transcription	Placenta	Placenta
12	chr5:112531800-112535400	Weak transcription	Fetal Stomach	stomach
13	chr5:112531800-112541000	Weak transcription	Aorta	Aorta
14	chr5:112532200-112538600	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:112533200-112536400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr5:112533200-112536600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:112533400-112536600	Enhancers	Ovary	ovary
18	chr5:112533400-112536600	Enhancers	Right Ventricle	heart
19	chr5:112533600-112536600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:112533800-112538600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:112533800-112541400	Weak transcription	Spleen	Spleen
22	chr5:112534000-112535400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:112534000-112536800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr5:112534000-112537200	Enhancers	Fetal Heart	heart
25	chr5:112534000-112538000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:112534200-112536200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:112534400-112537400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:112534400-112538600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:112534600-112535800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:112534600-112536200	Enhancers	Right Atrium	heart
31	chr5:112534800-112535800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:112534800-112535800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:112534800-112536000	Enhancers	Brain Substantia Nigra	brain
34	chr5:112534800-112536200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr5:112535000-112535400	Enhancers	Brain Germinal Matrix	brain
36	chr5:112535000-112535400	Enhancers	Brain Hippocampus Middle	brain
37	chr5:112535000-112535600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:112535000-112535600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:112535000-112535600	Enhancers	HMEC	breast
40	chr5:112535000-112535600	Enhancers	Osteobl	bone
41	chr5:112535000-112535800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:112535000-112535800	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr5:112535000-112536000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr5:112535000-112536200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:112535000-112536200	Enhancers	Brain Angular Gyrus	brain
46	chr5:112535000-112536200	Enhancers	NH-A	brain
47	chr5:112535000-112536200	Enhancers	NHDF-Ad	bronchial
48	chr5:112535000-112536400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:112535000-112536600	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr5:112535000-112536600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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