Variant report

Variant	rs17089267
Chromosome Location	chr4:69183791-69183792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10033058	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11726194	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727878	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13124352	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13130430	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1406694	0.87[ASN][1000 genomes]
rs17089252	0.81[ASN][1000 genomes]
rs1715080	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1715081	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1730873	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919898	0.84[ASN][1000 genomes]
rs2293594	0.82[ASN][1000 genomes]
rs2293595	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2319888	0.84[ASN][1000 genomes]
rs2319891	0.80[ASN][1000 genomes]
rs28656921	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34419508	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34452677	0.82[ASN][1000 genomes]
rs34500620	0.82[ASN][1000 genomes]
rs35632454	0.82[ASN][1000 genomes]
rs36098059	0.82[ASN][1000 genomes]
rs3797008	0.82[ASN][1000 genomes]
rs4428356	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4860929	0.81[ASN][1000 genomes]
rs56283078	0.84[ASN][1000 genomes]
rs57105149	0.83[ASN][1000 genomes]
rs57643586	0.85[ASN][1000 genomes]
rs58108365	0.85[ASN][1000 genomes]
rs62316045	0.85[ASN][1000 genomes]
rs6812178	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666993	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[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
rs17089267	YTHDC1	cis	uninvolved skin	skin_eQTL
rs17089267	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69176200-69203600	Strong transcription	Liver	Liver
2	chr4:69176200-69203600	Strong transcription	HSMM	muscle
3	chr4:69176200-69204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:69176200-69204200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:69176400-69184600	Strong transcription	Fetal Intestine Large	intestine
6	chr4:69176400-69184800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:69176400-69185200	Strong transcription	Primary B cells from cord blood	blood
8	chr4:69176400-69185200	Strong transcription	Stomach Smooth Muscle	stomach
9	chr4:69176400-69185400	Strong transcription	Brain Germinal Matrix	brain
10	chr4:69176400-69185400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr4:69176400-69185600	Strong transcription	Brain Anterior Caudate	brain
12	chr4:69176400-69186000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:69176400-69186000	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr4:69176400-69186000	Strong transcription	Adipose Nuclei	Adipose
15	chr4:69176400-69186200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:69176400-69188800	Strong transcription	GM12878-XiMat	blood
17	chr4:69176400-69203800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:69176400-69204000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:69176400-69204400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:69176400-69204600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:69176600-69185400	Strong transcription	Primary T cells from cord blood	blood
22	chr4:69176600-69185800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:69176600-69190200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:69176600-69198400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:69176600-69203600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:69176600-69204600	Strong transcription	Fetal Thymus	thymus
27	chr4:69176800-69185400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr4:69176800-69202200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:69176800-69203600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr4:69177200-69203600	Strong transcription	Placenta	Placenta
31	chr4:69177200-69203800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:69177200-69204200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:69177400-69184600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:69177400-69185000	Strong transcription	Fetal Lung	lung
35	chr4:69177400-69190000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:69177400-69204000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr4:69177600-69185000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:69177600-69185000	Strong transcription	Fetal Brain Female	brain
39	chr4:69177600-69186000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr4:69177800-69185600	Strong transcription	HMEC	breast
41	chr4:69177800-69186000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:69177800-69201200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr4:69177800-69203800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr4:69178000-69184600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:69178000-69185200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:69178000-69185200	Strong transcription	NHDF-Ad	bronchial
47	chr4:69178000-69185800	Strong transcription	Colon Smooth Muscle	Colon
48	chr4:69178000-69185800	Strong transcription	Fetal Kidney	kidney
49	chr4:69178000-69186000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr4:69178000-69186200	Strong transcription	Osteobl	bone

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