Variant report

Variant	rs5749283
Chromosome Location	chr22:31878581-31878582
allele	C/T
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	CEBPB	chr22:31878502-31878693	HepG2	liver:	n/a	chr22:31878618-31878629

No.	Distal block	Cell Line	Cell type
1	22:31864703-31891033..22:31936958-31958600	GM12878	blood:
2	chr22:31878049..31882754-chr22:31883144..31886598,7	MCF-7	breast:
3	22:31864703-31891033..22:31930706-31935473	GM12878	blood:
4	22:31864703-31891033..22:32347255-32351014	K562	blood:

Variant related genes	Relation type
RNU6-28P	TF binding region
ENSG00000214093	Chromatin interaction
ENSG00000229169	Chromatin interaction
ENSG00000238910	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000184708	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs13057504	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2273249	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2273251	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34538851	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34545960	0.90[AFR][1000 genomes]
rs5749267	0.90[AFR][1000 genomes]
rs5749268	0.90[AFR][1000 genomes]
rs5749270	0.90[AFR][1000 genomes]
rs5749286	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749291	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5749298	0.85[ASN][1000 genomes]
rs5753615	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs5753621	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5753628	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753631	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753648	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5753659	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753661	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753664	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753665	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753666	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753669	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753671	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7284622	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7285619	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8139625	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8142121	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9606843	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9606846	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9606847	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9606848	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9606852	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9609286	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9609295	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9609296	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9609297	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9609299	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9609301	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9609303	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9609304	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1060776	chr22:31869892-31900359	Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5749283	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs5749283	SFI1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:31815000-31883400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:31823600-31884600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr22:31847600-31881800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr22:31848800-31883000	Weak transcription	Fetal Heart	heart
7	chr22:31854800-31884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:31856800-31885000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:31858400-31884600	Weak transcription	Psoas Muscle	Psoas
10	chr22:31859400-31883800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr22:31859400-31884800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr22:31860000-31882600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr22:31860200-31884800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr22:31863400-31879400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr22:31864400-31879800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr22:31864400-31884400	Weak transcription	Brain Substantia Nigra	brain
17	chr22:31864400-31884600	Weak transcription	Aorta	Aorta
18	chr22:31864600-31884600	Weak transcription	Right Ventricle	heart
19	chr22:31865800-31880000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr22:31867400-31880800	Weak transcription	Colon Smooth Muscle	Colon
21	chr22:31867600-31884600	Weak transcription	Pancreas	Pancrea
22	chr22:31868800-31884200	Strong transcription	HSMM	muscle
23	chr22:31870000-31883400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr22:31870400-31883600	Strong transcription	Fetal Intestine Large	intestine
25	chr22:31870800-31879400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr22:31870800-31879800	Strong transcription	Dnd41	blood
27	chr22:31870800-31883600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr22:31870800-31884000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr22:31870800-31884400	Strong transcription	Fetal Thymus	thymus
30	chr22:31871000-31881600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr22:31871000-31884400	Strong transcription	Placenta	Placenta
32	chr22:31871200-31883800	Strong transcription	Fetal Intestine Small	intestine
33	chr22:31871600-31883000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr22:31871800-31879800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr22:31872200-31884200	Weak transcription	Hela-S3	cervix
36	chr22:31872600-31881400	Strong transcription	Adipose Nuclei	Adipose
37	chr22:31872600-31881600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr22:31872600-31884000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr22:31872600-31884200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr22:31872600-31884400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr22:31872800-31880400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr22:31872800-31882000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr22:31872800-31884400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr22:31872800-31884400	Strong transcription	Fetal Muscle Leg	muscle
45	chr22:31873000-31881600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr22:31873200-31883600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr22:31873200-31883800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr22:31873200-31884000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr22:31873400-31878800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr22:31873400-31881200	Strong transcription	Liver	Liver

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