Variant report

Variant	rs680503
Chromosome Location	chr5:112568212-112568213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112566555..112568778-chr5:112596838..112599414,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10070231	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11241196	0.81[CHB][hapmap]
rs11738528	0.82[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs12332686	0.83[AMR][1000 genomes]
rs12659754	0.88[CHB][hapmap];0.84[MEX][hapmap]
rs1822489	0.82[CHB][hapmap]
rs1867324	0.94[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs2120349	0.87[MEX][hapmap]
rs3846720	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs509237	0.88[CHB][hapmap];0.87[MEX][hapmap]
rs521929	0.86[AMR][1000 genomes]
rs522105	0.88[AMR][1000 genomes]
rs637634	0.82[ASW][hapmap];0.92[CHD][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes]
rs6865129	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7717906	0.83[MEX][hapmap]

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	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
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs680503	YTHDC2	cis	cerebellum	SCAN
rs680503	YTHDC2	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112548400-112581800	Weak transcription	Fetal Kidney	kidney
2	chr5:112557200-112585800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:112559000-112570000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:112559000-112571200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:112560800-112568400	Weak transcription	Fetal Stomach	stomach
6	chr5:112560800-112569000	Weak transcription	Osteobl	bone
7	chr5:112561200-112570400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:112561400-112568800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:112561600-112575000	Weak transcription	Right Ventricle	heart
10	chr5:112562200-112570400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:112565400-112572000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr5:112566000-112568400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr5:112566200-112572400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:112566400-112569000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:112566400-112569200	Enhancers	HMEC	breast
16	chr5:112566400-112569600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:112566400-112569800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:112566400-112571000	Enhancers	Adipose Nuclei	Adipose
19	chr5:112566400-112571200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr5:112566400-112572400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:112566400-112574000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:112566600-112569400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:112566800-112568600	Enhancers	HSMM	muscle
24	chr5:112566800-112569000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr5:112566800-112570600	Enhancers	NHDF-Ad	bronchial
26	chr5:112567000-112569200	Enhancers	HUVEC	blood vessel
27	chr5:112567000-112569400	Enhancers	Colon Smooth Muscle	Colon
28	chr5:112567200-112568800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:112567200-112569800	Enhancers	NH-A	brain
30	chr5:112567200-112571000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:112567200-112572400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:112567200-112572400	Enhancers	NHEK	skin
33	chr5:112567400-112569800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:112567400-112570000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:112567400-112571200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:112567400-112572800	Enhancers	Stomach Mucosa	stomach
37	chr5:112567400-112573200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:112567600-112568400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:112567600-112568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr5:112567800-112569400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:112567800-112569400	Enhancers	Liver	Liver
42	chr5:112567800-112569800	Enhancers	Fetal Heart	heart
43	chr5:112567800-112570800	Enhancers	Ovary	ovary
44	chr5:112568000-112568400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:112568000-112568600	Enhancers	Left Ventricle	heart
46	chr5:112568000-112568800	Weak transcription	Fetal Brain Female	brain
47	chr5:112568000-112568800	Enhancers	Fetal Muscle Leg	muscle
48	chr5:112568000-112568800	Enhancers	Right Atrium	heart
49	chr5:112568000-112569000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:112568000-112569000	Enhancers	Small Intestine	intestine

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