Variant report

Variant	rs6865129
Chromosome Location	chr5:112561002-112561003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10070231	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11241196	0.81[CHB][hapmap]
rs11738528	0.82[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12332686	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12659754	0.80[CEU][hapmap];0.88[CHB][hapmap];0.80[MEX][hapmap]
rs1822489	0.82[CHB][hapmap]
rs1867324	0.94[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs2120349	0.92[MEX][hapmap]
rs3846720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs509237	0.88[CHB][hapmap];0.92[MEX][hapmap]
rs521929	0.81[AMR][1000 genomes]
rs522105	0.83[AMR][1000 genomes]
rs637634	0.82[ASW][hapmap];0.92[CHD][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs680503	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	0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6865129	YTHDC2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112548400-112581800	Weak transcription	Fetal Kidney	kidney
2	chr5:112554200-112561600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:112554200-112564200	Weak transcription	Small Intestine	intestine
4	chr5:112555000-112566800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:112556600-112561800	Enhancers	Ovary	ovary
6	chr5:112557200-112585800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:112557400-112561800	Weak transcription	NHDF-Ad	bronchial
8	chr5:112557400-112564800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:112557600-112566400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:112557600-112566400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:112557800-112561800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:112557800-112562000	Weak transcription	NHEK	skin
13	chr5:112557800-112565200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:112557800-112566200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:112557800-112566400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:112557800-112566400	Weak transcription	HMEC	breast
17	chr5:112557800-112566600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:112558400-112561600	Enhancers	Right Ventricle	heart
19	chr5:112558600-112561600	Enhancers	Fetal Heart	heart
20	chr5:112558800-112568000	Weak transcription	Psoas Muscle	Psoas
21	chr5:112559000-112564800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:112559000-112568000	Weak transcription	Aorta	Aorta
23	chr5:112559000-112570000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:112559000-112571200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:112559200-112561600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:112559200-112562400	Enhancers	HUVEC	blood vessel
27	chr5:112559600-112561200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:112559600-112566400	Weak transcription	Adipose Nuclei	Adipose
29	chr5:112559800-112561400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:112559800-112565000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:112560000-112561400	Weak transcription	Left Ventricle	heart
32	chr5:112560000-112565400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:112560200-112561400	Enhancers	Liver	Liver
34	chr5:112560200-112568000	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:112560400-112561200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:112560400-112565400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:112560600-112561200	Weak transcription	Brain Substantia Nigra	brain
38	chr5:112560600-112561600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:112560600-112562200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:112560600-112566400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:112560800-112561200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:112560800-112561400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:112560800-112561600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:112560800-112561800	Weak transcription	NH-A	brain
45	chr5:112560800-112562200	Enhancers	Right Atrium	heart
46	chr5:112560800-112564800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:112560800-112568400	Weak transcription	Fetal Stomach	stomach
48	chr5:112560800-112569000	Weak transcription	Osteobl	bone
49	chr5:112561000-112565400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:112561000-112566800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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