Variant report

Variant	rs11162380
Chromosome Location	chr1:78202741-78202742
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1038983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10873953	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873955	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11162365	0.83[EUR][1000 genomes]
rs11162366	0.90[EUR][1000 genomes]
rs11162369	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11162370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11162372	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11162378	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11162383	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162386	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162387	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11578805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1166584	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1166586	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs12026939	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12132838	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12135104	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12142441	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12142671	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12717767	0.83[EUR][1000 genomes]
rs1389789	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1389790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1539739	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1565852	0.85[EUR][1000 genomes]
rs166770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1977900	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2031342	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs203229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2088058	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2147318	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2296227	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278832	0.84[ASN][1000 genomes]
rs278833	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs278834	0.85[ASN][1000 genomes]
rs278836	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278837	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs278840	0.93[ASN][1000 genomes]
rs278841	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278842	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278843	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278844	0.82[ASN][1000 genomes]
rs278845	0.81[EUR][1000 genomes]
rs278847	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs278851	0.81[ASN][1000 genomes]
rs278854	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278857	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278860	0.82[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278864	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs366467	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs370335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs371076	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3767037	0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767038	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4488068	0.91[ASN][1000 genomes]
rs4949661	0.92[EUR][1000 genomes]
rs4949814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs4949816	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs4949817	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4949818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4949822	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56688304	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs574973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6603956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6603958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6603960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6661656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6670660	0.92[EUR][1000 genomes]
rs6672200	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6674638	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6687501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6687596	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691317	0.91[EUR][1000 genomes]
rs6693100	0.83[EUR][1000 genomes]
rs6698151	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6699205	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6699311	1.00[JPT][hapmap]
rs717333	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7519946	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7521042	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7524866	0.93[CEU][hapmap]
rs7535781	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7543037	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7543125	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7545175	0.92[EUR][1000 genomes]
rs7546365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7552291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs7556227	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7556523	0.85[ASN][1000 genomes]
rs8179272	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs872342	0.83[JPT][hapmap]
rs9662527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription 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	34 gene(s)	inside rSNPs	diseases
3	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv1796958	chr1:78138955-78267421	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1798160	chr1:78149941-78267421	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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
7	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 target site	98 gene(s)	inside rSNPs	diseases
8	nsv508326	chr1:78184379-78234247	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11162380	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78171400-78206600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:78171600-78207400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:78171800-78205600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:78171800-78206800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr1:78171800-78206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:78171800-78206800	Strong transcription	Placenta	Placenta
7	chr1:78171800-78207000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:78171800-78207200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:78172000-78206000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:78172200-78206600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:78172400-78207600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:78172600-78205000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:78173800-78224400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:78174200-78207600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:78176400-78205200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:78176800-78205800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:78182400-78210200	Weak transcription	Psoas Muscle	Psoas
18	chr1:78182800-78210200	Weak transcription	Right Ventricle	heart
19	chr1:78185400-78203000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr1:78188000-78207800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:78189000-78204800	Weak transcription	Fetal Brain Male	brain
22	chr1:78189400-78210200	Weak transcription	NHEK	skin
23	chr1:78190600-78210800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:78190800-78203600	Weak transcription	Brain Germinal Matrix	brain
25	chr1:78191400-78206000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:78191600-78205600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:78191600-78210400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:78191600-78215600	Weak transcription	A549	lung
29	chr1:78192000-78215000	Weak transcription	HSMMtube	muscle
30	chr1:78192200-78222400	Weak transcription	Brain Substantia Nigra	brain
31	chr1:78192600-78204000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:78193000-78221200	Weak transcription	Brain Angular Gyrus	brain
33	chr1:78193200-78206600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:78193600-78222600	Weak transcription	Fetal Kidney	kidney
35	chr1:78194400-78205200	Weak transcription	Hela-S3	cervix
36	chr1:78194400-78209200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:78194400-78214400	Weak transcription	NHLF	lung
38	chr1:78194400-78223400	Weak transcription	NH-A	brain
39	chr1:78194600-78205000	Weak transcription	HMEC	breast
40	chr1:78194600-78215200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:78194800-78204600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:78194800-78207800	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:78194800-78212600	Weak transcription	Colonic Mucosa	Colon
44	chr1:78195000-78204400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:78195000-78213000	Weak transcription	HepG2	liver
46	chr1:78195200-78205600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:78195200-78210200	Weak transcription	Pancreas	Pancrea
48	chr1:78195200-78210400	Weak transcription	Lung	lung
49	chr1:78195200-78214000	Weak transcription	Small Intestine	intestine
50	chr1:78195400-78202800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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