Variant report

Variant	rs5754344
Chromosome Location	chr22:21963786-21963787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1034329	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11089620	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11089629	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12158299	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12168958	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12169001	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12484550	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs131656	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs131658	0.84[EUR][1000 genomes]
rs131664	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs131665	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs140489	0.85[EUR][1000 genomes]
rs140490	0.85[EUR][1000 genomes]
rs140491	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs140492	0.83[EUR][1000 genomes]
rs140498	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs140499	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1811069	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs181359	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs181360	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs181361	0.82[EUR][1000 genomes]
rs181363	0.86[EUR][1000 genomes]
rs181366	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2070512	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2256609	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266959	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2266961	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266963	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266964	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2283789	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2283790	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2298428	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298429	0.89[EUR][1000 genomes]
rs2876971	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4821104	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4821108	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4821112	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4821114	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4821116	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4821124	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4821130	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5749485	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5749493	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5749495	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749502	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754100	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5754102	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5754166	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754177	0.89[AMR][1000 genomes]
rs5754217	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5754234	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754238	0.89[EUR][1000 genomes]
rs5754295	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754323	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754352	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5754422	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5754426	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59391722	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5994638	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5998509	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5998576	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5998599	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5998619	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5998644	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5998672	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66534072	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73166619	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73166622	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73166630	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73166632	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs738127	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs738128	0.88[EUR][1000 genomes]
rs7444	0.92[EUR][1000 genomes]
rs7445	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8137950	0.88[EUR][1000 genomes]
rs8139079	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs878825	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9619386	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9621715	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914458	chr22:21747678-22070489	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
2	nsv482690	chr22:21807513-22016791	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
3	esv1823866	chr22:21928916-22131125	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
4	nsv948603	chr22:21928916-22601814	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
5	nsv948902	chr22:21928916-22657900	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	426 gene(s)	inside rSNPs	diseases
6	nsv1063962	chr22:21939722-22934593	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
7	nsv1058617	chr22:21939922-22934454	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
8	nsv529694	chr22:21957411-22905068	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5754344	UBE2L3	Cis_1M	lymphoblastoid	RTeQTL
rs5754344	UBE2L3	cis	multi-tissue	Pritchard
rs5754344	CCDC116	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:21937800-21965400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:21939600-21983200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr22:21946400-21980200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:21948800-21965200	Weak transcription	Fetal Kidney	kidney
5	chr22:21949200-21976600	Weak transcription	Fetal Brain Male	brain
6	chr22:21949400-21965400	Weak transcription	Hela-S3	cervix
7	chr22:21949600-21965200	Weak transcription	Colon Smooth Muscle	Colon
8	chr22:21949800-21965200	Weak transcription	Brain Anterior Caudate	brain
9	chr22:21949800-21965400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:21949800-21965400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr22:21949800-21968800	Weak transcription	Stomach Mucosa	stomach
12	chr22:21950000-21965200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr22:21950000-21965200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr22:21950000-21965400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:21950000-21978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr22:21950200-21965200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr22:21950200-21965200	Weak transcription	NH-A	brain
18	chr22:21950200-21965400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr22:21950600-21964000	Weak transcription	HUVEC	blood vessel
20	chr22:21950600-21964400	Weak transcription	Fetal Brain Female	brain
21	chr22:21950600-21965200	Weak transcription	Fetal Lung	lung
22	chr22:21950600-21965400	Weak transcription	Aorta	Aorta
23	chr22:21950800-21964400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr22:21951200-21964400	Weak transcription	NHLF	lung
25	chr22:21951200-21964600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr22:21951200-21964600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr22:21951200-21965000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr22:21951200-21965400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr22:21951400-21965200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr22:21951800-21964200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr22:21952000-21964200	Weak transcription	Osteobl	bone
32	chr22:21952800-21965400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr22:21953800-21964400	Weak transcription	Liver	Liver
34	chr22:21953800-21964400	Weak transcription	Brain Angular Gyrus	brain
35	chr22:21954000-21964000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr22:21954000-21965200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr22:21954000-21965400	Weak transcription	Brain Substantia Nigra	brain
38	chr22:21954200-21964400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr22:21954200-21964400	Weak transcription	NHDF-Ad	bronchial
40	chr22:21954400-21963800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr22:21957000-21964400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr22:21957000-21965200	Weak transcription	HSMM	muscle
43	chr22:21957000-21965400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr22:21957200-21963800	Weak transcription	Thymus	Thymus
45	chr22:21957200-21963800	Weak transcription	HepG2	liver
46	chr22:21957200-21964400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr22:21957200-21965400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr22:21957200-21965600	Weak transcription	HSMMtube	muscle
49	chr22:21957400-21964200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr22:21957400-21964400	Weak transcription	Duodenum Mucosa	Duodenum

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