Variant report

Variant	rs492346
Chromosome Location	chr5:112617337-112617338
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	chr5:112616654..112618757-chr5:112626610..112628435,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10067046	0.88[MEX][hapmap]
rs10076501	0.84[MEX][hapmap]
rs10900684	0.84[MEX][hapmap]
rs13153071	0.84[MEX][hapmap]
rs13190054	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1517210	0.84[ASW][hapmap]
rs164253	0.81[AFR][1000 genomes]
rs17327526	0.82[ASW][hapmap];0.83[LWK][hapmap]
rs1838207	0.89[AMR][1000 genomes]
rs255856	0.84[ASW][hapmap];0.96[MEX][hapmap]
rs26983	0.81[AMR][1000 genomes]
rs27566	0.84[ASW][hapmap];0.96[MEX][hapmap]
rs3857435	0.84[ASW][hapmap];0.96[MEX][hapmap]
rs4108702	0.84[MEX][hapmap]
rs4705812	0.84[MEX][hapmap]
rs485210	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6594700	0.83[MEX][hapmap]
rs675353	0.84[ASW][hapmap];0.88[MEX][hapmap]
rs7715342	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7722276	0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1018078	chr5:112615220-112657404	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active 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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs492346	YTHDC2	cis	cerebellum	SCAN
rs492346	YTHDC2	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
2	chr5:112600200-112618000	Weak transcription	Fetal Kidney	kidney
3	chr5:112608000-112628200	Weak transcription	HMEC	breast
4	chr5:112610000-112628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:112610800-112623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:112611000-112618000	Weak transcription	Fetal Stomach	stomach
7	chr5:112611000-112628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:112611200-112618000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:112612000-112618000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:112612000-112623800	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:112612000-112625200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:112612200-112625200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:112612400-112618400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:112613400-112618000	Enhancers	Ovary	ovary
15	chr5:112614200-112625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:112614400-112617400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:112615000-112625200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:112615200-112617400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:112615400-112617400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:112616400-112617600	Enhancers	HUVEC	blood vessel
21	chr5:112616400-112617800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:112616400-112618400	Enhancers	Adipose Nuclei	Adipose
23	chr5:112616400-112619000	Enhancers	Liver	Liver
24	chr5:112616400-112619200	Enhancers	Brain Anterior Caudate	brain
25	chr5:112616600-112618000	Enhancers	Brain Hippocampus Middle	brain
26	chr5:112616600-112618000	Weak transcription	Spleen	Spleen
27	chr5:112616600-112618400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr5:112616600-112618400	Enhancers	Stomach Smooth Muscle	stomach
29	chr5:112616600-112620000	Enhancers	Fetal Heart	heart
30	chr5:112616800-112617400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:112616800-112617400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr5:112616800-112618000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:112616800-112618000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:112616800-112619000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:112616800-112623400	Weak transcription	NHEK	skin
36	chr5:112616800-112623800	Weak transcription	Esophagus	oesophagus
37	chr5:112617000-112617800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr5:112617000-112619200	Enhancers	Fetal Lung	lung
39	chr5:112617000-112619400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr5:112617000-112619400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr5:112617000-112619800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr5:112617000-112620400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr5:112617000-112622000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:112617200-112617600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:112617200-112618000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:112617200-112618000	Weak transcription	Left Ventricle	heart
47	chr5:112617200-112618400	Weak transcription	Right Ventricle	heart
48	chr5:112617200-112618600	Weak transcription	Brain Substantia Nigra	brain
49	chr5:112617200-112618600	Weak transcription	Right Atrium	heart
50	chr5:112617200-112619000	Enhancers	Cortex derived primary cultured neurospheres	brain

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