Variant report

Variant	rs553212
Chromosome Location	chr18:195405-195406
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	POLR2A	chr18:195398-195561	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
USP14	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11663945	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11877873	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274276	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1784375	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132798	1.00[ASN][1000 genomes]
rs34132492	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35228921	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472780	1.00[ASN][1000 genomes]
rs477718	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478096	1.00[ASN][1000 genomes]
rs484168	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485211	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489947	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500596	0.95[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505610	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507184	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510589	0.94[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511573	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527035	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530926	0.93[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs533992	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537202	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538786	0.95[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541733	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543184	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547590	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551835	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562117	0.90[EUR][1000 genomes]
rs562748	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563155	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565653	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566748	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572981	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585793	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592537	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598162	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598617	1.00[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605049	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605877	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609865	0.85[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs610712	0.93[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617421	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621979	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636436	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644363	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645560	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650695	1.00[ASN][1000 genomes]
rs652079	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652504	0.95[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653301	1.00[ASN][1000 genomes]
rs654019	0.83[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655983	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659997	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674727	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680201	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680418	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688023	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692846	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
rs553212	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	chr18:159600-199000	Weak transcription	Colonic Mucosa	Colon
2	chr18:159800-199200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:160000-203000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:160200-210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr18:160200-218000	Weak transcription	Stomach Mucosa	stomach
6	chr18:160200-218400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr18:160600-203200	Weak transcription	Psoas Muscle	Psoas
8	chr18:165600-196800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr18:168800-196800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr18:168800-198200	Weak transcription	Spleen	Spleen
11	chr18:171400-196800	Weak transcription	Esophagus	oesophagus
12	chr18:171400-196800	Weak transcription	Gastric	stomach
13	chr18:171400-199200	Weak transcription	Right Ventricle	heart
14	chr18:172600-196800	Weak transcription	HSMMtube	muscle
15	chr18:174000-198000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr18:178200-210800	Weak transcription	Pancreas	Pancrea
17	chr18:180800-196600	Weak transcription	Fetal Brain Female	brain
18	chr18:180800-197400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr18:180800-197600	Weak transcription	Fetal Brain Male	brain
20	chr18:180800-205000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr18:180800-205400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:181000-196800	Weak transcription	Brain Angular Gyrus	brain
23	chr18:181000-210800	Weak transcription	Small Intestine	intestine
24	chr18:181400-196600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr18:181400-197000	Weak transcription	Brain Germinal Matrix	brain
26	chr18:181600-197000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr18:182000-196800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr18:182000-196800	Weak transcription	Fetal Kidney	kidney
29	chr18:182200-199000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr18:182400-196600	Weak transcription	Hela-S3	cervix
31	chr18:182800-196400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr18:182800-196800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr18:182800-200200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr18:184200-195600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr18:184200-196800	Weak transcription	HUVEC	blood vessel
36	chr18:184400-197000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr18:184600-196600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr18:184600-197000	Weak transcription	Colon Smooth Muscle	Colon
39	chr18:184600-197000	Weak transcription	HSMM	muscle
40	chr18:186400-195600	Weak transcription	Fetal Intestine Large	intestine
41	chr18:186400-196600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr18:186400-196600	Weak transcription	Adipose Nuclei	Adipose
43	chr18:186400-196600	Weak transcription	NHLF	lung
44	chr18:186600-196400	Weak transcription	Fetal Intestine Small	intestine
45	chr18:186600-196600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr18:186600-196600	Weak transcription	Lung	lung
47	chr18:186600-196800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr18:186600-196800	Weak transcription	Aorta	Aorta
49	chr18:186600-196800	Weak transcription	Left Ventricle	heart
50	chr18:186600-196800	Weak transcription	Thymus	Thymus

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