Variant report

Variant	rs12649108
Chromosome Location	chr4:69181942-69181943
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17089252	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293594	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34147623	0.81[EUR][1000 genomes]
rs34346807	0.81[EUR][1000 genomes]
rs4860929	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4860931	0.82[ASN][1000 genomes]
rs56283078	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57105149	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57643586	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58108365	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62316045	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv461546	chr4:69049643-69223057	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv594506	chr4:69049643-69223057	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2757061	chr4:69178920-69631668	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12649108	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL
rs12649108	MUC7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69174000-69182000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:69174000-69182000	Weak transcription	Esophagus	oesophagus
3	chr4:69174000-69182600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:69174400-69182000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:69175000-69182000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:69175000-69182000	Weak transcription	Thymus	Thymus
7	chr4:69175000-69182400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:69176000-69182400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:69176200-69182000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:69176200-69182000	Weak transcription	Pancreas	Pancrea
11	chr4:69176200-69182200	Weak transcription	Gastric	stomach
12	chr4:69176200-69203600	Strong transcription	Liver	Liver
13	chr4:69176200-69203600	Strong transcription	HSMM	muscle
14	chr4:69176200-69204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:69176200-69204200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:69176400-69182000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:69176400-69183600	Strong transcription	Primary hematopoietic stem cells	blood
18	chr4:69176400-69184600	Strong transcription	Fetal Intestine Large	intestine
19	chr4:69176400-69184800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:69176400-69185200	Strong transcription	Primary B cells from cord blood	blood
21	chr4:69176400-69185200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr4:69176400-69185400	Strong transcription	Brain Germinal Matrix	brain
23	chr4:69176400-69185400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr4:69176400-69185600	Strong transcription	Brain Anterior Caudate	brain
25	chr4:69176400-69186000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:69176400-69186000	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr4:69176400-69186000	Strong transcription	Adipose Nuclei	Adipose
28	chr4:69176400-69186200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:69176400-69188800	Strong transcription	GM12878-XiMat	blood
30	chr4:69176400-69203800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:69176400-69204000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:69176400-69204400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:69176400-69204600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:69176600-69182000	Weak transcription	Fetal Heart	heart
35	chr4:69176600-69182800	Strong transcription	NH-A	brain
36	chr4:69176600-69185400	Strong transcription	Primary T cells from cord blood	blood
37	chr4:69176600-69185800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:69176600-69190200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:69176600-69198400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:69176600-69203600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:69176600-69204600	Strong transcription	Fetal Thymus	thymus
42	chr4:69176800-69182000	Weak transcription	Aorta	Aorta
43	chr4:69176800-69185400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr4:69176800-69202200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:69176800-69203600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr4:69177000-69182000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:69177200-69182400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr4:69177200-69203600	Strong transcription	Placenta	Placenta
49	chr4:69177200-69203800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:69177200-69204200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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