Variant report

Variant	rs1822489
Chromosome Location	chr5:112542527-112542528
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	chr5:112537173..112539985-chr5:112540177..112543162,2	K562	blood:
2	chr5:112530552..112532228-chr5:112541838..112543468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11241196	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11738528	0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12332686	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12656003	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12659754	0.80[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867324	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]
rs3846720	0.82[CHB][hapmap]
rs680503	0.82[CHB][hapmap]
rs6865129	0.82[CHB][hapmap]
rs6899208	0.81[EUR][1000 genomes];0.89[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
rs1822489	YTHDC2	cis	parietal	SCAN
rs1822489	YTHDC2	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112538800-112544200	Weak transcription	Fetal Kidney	kidney
2	chr5:112539000-112547200	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:112539200-112549200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:112539200-112554000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:112539400-112542600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:112539400-112548000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:112539400-112548000	Weak transcription	Fetal Stomach	stomach
8	chr5:112539600-112544800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:112539800-112546800	Enhancers	Fetal Heart	heart
10	chr5:112539800-112548200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:112540000-112547800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:112540000-112548000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:112540400-112548800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:112540600-112547200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:112540600-112548000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:112540800-112547800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:112540800-112548800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr5:112540800-112553400	Weak transcription	Brain Angular Gyrus	brain
19	chr5:112541000-112547800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:112541200-112543200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:112541200-112543600	Weak transcription	Psoas Muscle	Psoas
22	chr5:112541200-112548000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:112541200-112548200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:112541400-112542600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:112541600-112543000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:112541600-112543400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:112541600-112547200	Weak transcription	Brain Anterior Caudate	brain
28	chr5:112541800-112542800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:112541800-112542800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:112541800-112542800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:112541800-112542800	Weak transcription	Brain Hippocampus Middle	brain
32	chr5:112541800-112543200	Enhancers	Liver	Liver
33	chr5:112541800-112543400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:112541800-112547000	Weak transcription	Fetal Lung	lung
35	chr5:112541800-112547200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:112541800-112547200	Weak transcription	Adipose Nuclei	Adipose
37	chr5:112541800-112548200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:112541800-112550400	Weak transcription	Esophagus	oesophagus
39	chr5:112542000-112542800	Weak transcription	Right Atrium	heart
40	chr5:112542000-112543000	Weak transcription	Brain Substantia Nigra	brain
41	chr5:112542000-112543200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:112542000-112543400	Weak transcription	HMEC	breast
43	chr5:112542000-112543600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:112542000-112543600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:112542000-112543600	Weak transcription	Left Ventricle	heart
46	chr5:112542000-112545000	Weak transcription	Ovary	ovary
47	chr5:112542000-112545000	Weak transcription	Right Ventricle	heart
48	chr5:112542000-112546600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:112542000-112547200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:112542000-112547800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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