Variant report

Variant	rs485210
Chromosome Location	chr5:112629887-112629888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112628328..112630254-chr5:112656025..112657722,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

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];0.89[AMR][1000 genomes]
rs1517210	0.84[ASW][hapmap]
rs164253	0.81[AFR][1000 genomes]
rs17327526	0.82[ASW][hapmap];1.00[LWK][hapmap]
rs1838207	0.88[AMR][1000 genomes]
rs1845290	0.82[AMR][1000 genomes]
rs2165928	0.80[AMR][1000 genomes]
rs255856	0.84[ASW][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap]
rs255867	0.80[AMR][1000 genomes]
rs26983	0.84[AMR][1000 genomes]
rs27566	0.84[ASW][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap]
rs348937	0.87[GIH][hapmap]
rs3857435	0.84[ASW][hapmap];0.96[MEX][hapmap]
rs4108702	0.84[MEX][hapmap]
rs4705812	0.84[MEX][hapmap]
rs4705813	0.81[AMR][1000 genomes]
rs492346	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];0.83[LWK][hapmap];0.88[MEX][hapmap]
rs6869097	0.81[AMR][1000 genomes]
rs6875238	0.81[AMR][1000 genomes]
rs6879612	0.83[AMR][1000 genomes]
rs7715342	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7722276	1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[AFR][1000 genomes];0.89[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
rs485210	YTHDC2	cis	cerebellum	SCAN
rs485210	YTHDC2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112626800-112631400	Active TSS	Ovary	ovary
2	chr5:112627200-112631200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:112627400-112631000	Active TSS	Psoas Muscle	Psoas
4	chr5:112628200-112630800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:112628200-112630800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr5:112628200-112631000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:112628200-112631000	Active TSS	Brain Hippocampus Middle	brain
8	chr5:112628200-112631000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr5:112628200-112631000	Active TSS	Brain Substantia Nigra	brain
10	chr5:112628200-112631000	Active TSS	Right Atrium	heart
11	chr5:112628200-112631000	Active TSS	Stomach Smooth Muscle	stomach
12	chr5:112628200-112631200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:112628200-112631200	Active TSS	NHDF-Ad	bronchial
14	chr5:112628400-112631000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:112628400-112631000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:112628400-112631000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:112628400-112631200	Active TSS	Fetal Muscle Trunk	muscle
18	chr5:112628400-112631200	Active TSS	Left Ventricle	heart
19	chr5:112628600-112630200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:112628600-112630600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:112628600-112630600	Active TSS	Lung	lung
22	chr5:112628600-112630800	Active TSS	Brain Angular Gyrus	brain
23	chr5:112628600-112630800	Active TSS	Esophagus	oesophagus
24	chr5:112628600-112630800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
25	chr5:112628600-112631000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr5:112628600-112631000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr5:112628600-112631000	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr5:112628600-112631200	Active TSS	Rectal Smooth Muscle	rectum
29	chr5:112628600-112631400	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr5:112628800-112630200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
31	chr5:112628800-112631000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:112628800-112631200	Active TSS	Gastric	stomach
33	chr5:112629000-112630200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr5:112629000-112630200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
35	chr5:112629000-112630600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:112629000-112630800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
37	chr5:112629000-112630800	Active TSS	NHEK	skin
38	chr5:112629000-112631000	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr5:112629000-112631000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:112629000-112631000	Active TSS	Fetal Stomach	stomach
41	chr5:112629000-112631200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:112629000-112631200	Active TSS	Colon Smooth Muscle	Colon
43	chr5:112629000-112631400	Bivalent/Poised TSS	Thymus	Thymus
44	chr5:112629200-112630200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:112629200-112630400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr5:112629200-112630600	Active TSS	Small Intestine	intestine
47	chr5:112629200-112630800	Active TSS	Liver	Liver
48	chr5:112629200-112630800	Bivalent/Poised TSS	Stomach Mucosa	stomach
49	chr5:112629200-112630800	Active TSS	HMEC	breast
50	chr5:112629200-112631000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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