Variant report

Variant	rs17089252
Chromosome Location	chr4:69176962-69176963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10033058	0.85[ASN][1000 genomes]
rs12649108	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17089267	0.81[ASN][1000 genomes]
rs1715080	0.82[ASN][1000 genomes]
rs1715081	0.81[ASN][1000 genomes]
rs1730873	0.81[ASN][1000 genomes]
rs1996598	0.82[AFR][1000 genomes]
rs2293594	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293595	0.85[ASN][1000 genomes]
rs34147623	0.82[EUR][1000 genomes]
rs34346807	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4860929	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4860931	0.84[ASN][1000 genomes]
rs56283078	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57105149	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57643586	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58108365	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62298442	0.81[AFR][1000 genomes]
rs62316045	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6812178	0.81[ASN][1000 genomes]
rs7659406	0.93[YRI][hapmap];0.82[AFR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17089252	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL
rs17089252	MUC7	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69167000-69179400	Weak transcription	HepG2	liver
2	chr4:69173400-69178600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:69174000-69178000	Weak transcription	Osteobl	bone
4	chr4:69174000-69182000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:69174000-69182000	Weak transcription	Esophagus	oesophagus
6	chr4:69174000-69182600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:69174400-69177600	Weak transcription	NHLF	lung
8	chr4:69174400-69179800	Weak transcription	Fetal Intestine Small	intestine
9	chr4:69174400-69179800	Weak transcription	Fetal Stomach	stomach
10	chr4:69174400-69182000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:69174800-69177800	Weak transcription	HMEC	breast
12	chr4:69174800-69178800	Weak transcription	Lung	lung
13	chr4:69175000-69177200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:69175000-69177200	Weak transcription	Placenta	Placenta
15	chr4:69175000-69177800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:69175000-69178000	Weak transcription	Fetal Kidney	kidney
17	chr4:69175000-69178000	Weak transcription	HUVEC	blood vessel
18	chr4:69175000-69178200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:69175000-69178800	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:69175000-69179200	Weak transcription	Psoas Muscle	Psoas
21	chr4:69175000-69179200	Weak transcription	NHEK	skin
22	chr4:69175000-69179600	Weak transcription	Fetal Brain Male	brain
23	chr4:69175000-69182000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:69175000-69182000	Weak transcription	Thymus	Thymus
25	chr4:69175000-69182400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:69175200-69177400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:69175200-69177400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr4:69175200-69177800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr4:69175200-69178200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:69175200-69178200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:69175200-69178200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:69175200-69178800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:69175200-69178800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:69175200-69180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:69175400-69177000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:69175400-69177200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:69175400-69177600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:69175400-69178000	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:69175400-69178200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:69175400-69179000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:69175400-69179400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:69175600-69177400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:69175600-69177600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr4:69175800-69177400	Weak transcription	Fetal Lung	lung
45	chr4:69176000-69177600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:69176000-69177600	Weak transcription	Fetal Brain Female	brain
47	chr4:69176000-69177600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr4:69176000-69182400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:69176200-69177800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr4:69176200-69178000	Weak transcription	Rectal Mucosa Donor 31	rectum

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