Variant report

Variant	rs490425
Chromosome Location	chr18:165022-165023
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:164137..168777-chr18:169771..171938,5	K562	blood:
2	chr18:164894..167848-chr18:172518..174416,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12960837	0.90[ASN][1000 genomes]
rs1299113	0.88[ASN][1000 genomes]
rs1784380	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1785049	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2509447	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs471274	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs477066	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs481077	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs484863	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs489560	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs489577	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs513402	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs513894	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs514003	0.82[EUR][1000 genomes]
rs523239	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs535992	0.83[EUR][1000 genomes]
rs545447	0.91[ASN][1000 genomes]
rs557249	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs577454	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs579219	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585578	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs599361	0.80[EUR][1000 genomes]
rs600022	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs600220	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs605826	0.84[ASN][1000 genomes]
rs620970	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs621782	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs631343	0.84[ASN][1000 genomes]
rs644438	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs655781	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs663186	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs672856	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7238463	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7241427	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909285	chr18:10001-196829	Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
2	nsv1059917	chr18:11543-175067	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1059509	chr18:11543-190140	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
4	nsv1064673	chr18:11543-249310	Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1061730	chr18:11543-322183	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1059645	chr18:11543-326679	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv576227	chr18:52933-322183	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1064150	chr18:99036-321710	Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1055303	chr18:112328-304352	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv543527	chr18:112328-304352	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv543530	chr18:112528-932674	Weak transcription Strong transcription Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
12	nsv1067102	chr18:112528-984688	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
13	nsv543531	chr18:112528-984688	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv1066441	chr18:136228-249310	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
15	nsv1057029	chr18:141491-356238	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
16	nsv1066995	chr18:141491-415027	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
17	nsv1064735	chr18:141491-483651	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
18	nsv1062680	chr18:141491-549166	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
19	nsv1067218	chr18:141491-603796	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv543544	chr18:141491-675519	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
21	nsv1064998	chr18:141491-1095845	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
22	nsv543545	chr18:141491-1095845	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
23	nsv1057105	chr18:143546-235928	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
24	nsv531216	chr18:148763-293736	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
25	nsv532441	chr18:148763-1108997	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
26	nsv530373	chr18:148963-533693	Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
27	esv3406270	chr18:151001-180091	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
28	nsv482910	chr18:161390-305010	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs490425	USP14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:159400-186000	Weak transcription	Aorta	Aorta
2	chr18:159600-166800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr18:159600-168400	Weak transcription	Lung	lung
4	chr18:159600-169800	Weak transcription	Esophagus	oesophagus
5	chr18:159600-170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:159600-199000	Weak transcription	Colonic Mucosa	Colon
7	chr18:159800-165400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr18:159800-191400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr18:159800-199200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:160000-165400	Weak transcription	Colon Smooth Muscle	Colon
11	chr18:160000-168400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr18:160000-203000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr18:160200-169000	Weak transcription	Right Ventricle	heart
14	chr18:160200-180400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr18:160200-210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr18:160200-218000	Weak transcription	Stomach Mucosa	stomach
17	chr18:160200-218400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr18:160400-165200	Weak transcription	Primary B cells from cord blood	blood
19	chr18:160400-167000	Weak transcription	Left Ventricle	heart
20	chr18:160600-165200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr18:160600-165800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr18:160600-167000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr18:160600-167200	Weak transcription	Pancreas	Pancrea
24	chr18:160600-168200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr18:160600-169800	Weak transcription	Thymus	Thymus
26	chr18:160600-170600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr18:160600-203200	Weak transcription	Psoas Muscle	Psoas
28	chr18:160800-165600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr18:160800-165600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr18:160800-165600	Weak transcription	Brain Hippocampus Middle	brain
31	chr18:160800-165800	Weak transcription	Fetal Lung	lung
32	chr18:160800-176600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr18:160800-183600	Weak transcription	Fetal Heart	heart
34	chr18:160800-183600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr18:161000-165600	Weak transcription	Brain Angular Gyrus	brain
36	chr18:161000-165600	Weak transcription	Brain Substantia Nigra	brain
37	chr18:161000-168400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr18:161000-174200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr18:161000-178400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr18:161000-185600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr18:161200-165400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr18:161200-167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr18:161200-168400	Weak transcription	Spleen	Spleen
44	chr18:161200-175200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr18:161400-166800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr18:161400-170400	Weak transcription	Gastric	stomach
47	chr18:161400-172200	Weak transcription	Fetal Brain Male	brain
48	chr18:161400-175600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr18:161400-180400	Weak transcription	Small Intestine	intestine
50	chr18:161600-165400	Weak transcription	Brain Cingulate Gyrus	brain

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