Variant report

Variant	rs1867324
Chromosome Location	chr5:112539955-112539956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr5:112539944-112539967	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr5:112537418-112540905	SK-N-SH	brain:	n/a	n/a
3	MAFK	chr5:112539755-112539965	HepG2	liver:	n/a	n/a
4	MYC	chr5:112539862-112539977	MCF10A-Er-Src	breast:	n/a	chr5:112539878-112539887
5	EP300	chr5:112538047-112541128	SK-N-SH	brain:	n/a	chr5:112540678-112540691
6	KAP1	chr5:112538726-112540002	HEK293	kidney:	n/a	chr5:112538767-112538775

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112537173..112539985-chr5:112540177..112543162,2	K562	blood:
2	chr5:112538594..112540259-chr5:112848065..112850694,2	MCF-7	breast:

Variant related genes	Relation type
MCC	TF binding region
ENSG00000171444	Chromatin interaction
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10070231	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11241196	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11738528	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332686	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12656003	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12659754	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13159076	0.82[ASW][hapmap]
rs1822489	0.92[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2120349	0.87[MEX][hapmap]
rs3846720	0.94[CHB][hapmap];0.80[AMR][1000 genomes]
rs509237	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs637634	0.82[ASW][hapmap]
rs680503	0.94[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs6865129	0.94[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs6899208	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1867324	YTHDC2	cis	cerebellum	SCAN
rs1867324	YTHDC2	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112522600-112541000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:112531800-112541000	Weak transcription	Aorta	Aorta
3	chr5:112533800-112541400	Weak transcription	Spleen	Spleen
4	chr5:112535600-112540400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:112535600-112540600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:112535800-112540600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:112536200-112540200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:112536400-112541800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:112537000-112540400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:112537200-112541800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr5:112537200-112542000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr5:112537400-112541200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr5:112537400-112541800	Enhancers	Adipose Nuclei	Adipose
14	chr5:112537600-112540000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr5:112537600-112541200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr5:112538000-112541400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:112538400-112540400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:112538400-112541000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:112538400-112541200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:112538600-112540000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:112538600-112540000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:112538600-112540000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:112538600-112540400	Flanking Active TSS	NHEK	skin
24	chr5:112538600-112541800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:112538600-112542000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:112538800-112540000	Active TSS	Esophagus	oesophagus
27	chr5:112538800-112541800	Enhancers	Brain Cingulate Gyrus	brain
28	chr5:112538800-112542000	Enhancers	HMEC	breast
29	chr5:112538800-112544200	Weak transcription	Fetal Kidney	kidney
30	chr5:112539000-112540000	Active TSS	Brain Substantia Nigra	brain
31	chr5:112539000-112541400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:112539000-112542000	Enhancers	Right Ventricle	heart
33	chr5:112539000-112547200	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:112539200-112540200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:112539200-112540200	Weak transcription	Left Ventricle	heart
36	chr5:112539200-112540200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:112539200-112540400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:112539200-112540600	Weak transcription	Placenta	Placenta
39	chr5:112539200-112540800	Enhancers	Brain Angular Gyrus	brain
40	chr5:112539200-112541000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr5:112539200-112541000	Enhancers	Hela-S3	cervix
42	chr5:112539200-112541200	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr5:112539200-112541400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:112539200-112541600	Weak transcription	Gastric	stomach
45	chr5:112539200-112541600	Weak transcription	Lung	lung
46	chr5:112539200-112541800	Enhancers	Brain Hippocampus Middle	brain
47	chr5:112539200-112549200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr5:112539200-112554000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr5:112539400-112540000	Enhancers	NH-A	brain
50	chr5:112539400-112540200	Weak transcription	Ovary	ovary

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