Variant report

Variant	rs12090729
Chromosome Location	chr1:78286674-78286675
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78285341..78286851-chr1:78287650..78290404,2	K562	blood:
2	chr1:78278539..78280427-chr1:78285432..78287469,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10873953	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10873954	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873955	1.00[ASN][1000 genomes]
rs11162368	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11162370	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11162374	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11162378	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11162383	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162384	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162386	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162387	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1166586	0.98[ASN][1000 genomes]
rs1166589	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12132838	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12135104	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12142441	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12717768	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1389789	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1389790	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1539739	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166770	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2031342	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs203229	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2296227	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs278832	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278834	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs278837	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278840	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278841	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278842	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278844	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278848	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278850	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs278851	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278855	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278856	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs278860	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278863	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3767037	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3767038	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4488068	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4949817	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4949818	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4949822	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56688304	0.85[ASN][1000 genomes]
rs574973	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6603958	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6603960	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6661656	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6672200	0.84[ASN][1000 genomes]
rs6687501	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6687596	0.85[ASN][1000 genomes]
rs6699205	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6699311	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs717333	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7519946	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7535781	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7536206	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543037	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543125	1.00[ASN][1000 genomes]
rs7546365	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7556227	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556523	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8179272	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872342	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9988619	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12090729	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78246400-78287400	Weak transcription	Fetal Heart	heart
2	chr1:78248600-78288200	Weak transcription	Small Intestine	intestine
3	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
4	chr1:78254400-78287200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:78266000-78298000	Weak transcription	K562	blood
6	chr1:78266200-78299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:78266200-78299200	Weak transcription	Pancreas	Pancrea
8	chr1:78268400-78291200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:78273400-78289600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:78273600-78290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:78273600-78290000	Weak transcription	Psoas Muscle	Psoas
12	chr1:78273600-78293200	Weak transcription	Brain Germinal Matrix	brain
13	chr1:78274600-78288600	Weak transcription	HepG2	liver
14	chr1:78274600-78290800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:78274800-78297400	Weak transcription	Brain Substantia Nigra	brain
16	chr1:78274800-78297600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:78274800-78298000	Weak transcription	Fetal Kidney	kidney
18	chr1:78275000-78289000	Weak transcription	A549	lung
19	chr1:78275000-78312800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:78277000-78290200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:78277400-78291200	Strong transcription	Fetal Intestine Small	intestine
22	chr1:78277600-78292600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr1:78278400-78289600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:78278600-78287000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:78278800-78287400	Strong transcription	Placenta	Placenta
26	chr1:78278800-78288800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:78278800-78290200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:78279200-78288000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:78279200-78288000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:78279200-78288200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:78279200-78288200	Strong transcription	Liver	Liver
32	chr1:78279200-78288400	Strong transcription	Fetal Intestine Large	intestine
33	chr1:78279200-78288800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr1:78279200-78289600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:78279200-78300400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:78279400-78289600	Strong transcription	Fetal Thymus	thymus
37	chr1:78279400-78289800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:78279400-78290600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:78279800-78294800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:78280000-78292200	Weak transcription	Aorta	Aorta
41	chr1:78280400-78289400	Weak transcription	NHLF	lung
42	chr1:78280400-78297400	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:78280600-78287000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:78280600-78291000	Weak transcription	Brain Angular Gyrus	brain
45	chr1:78280600-78292600	Weak transcription	Lung	lung
46	chr1:78280600-78298000	Weak transcription	Fetal Brain Male	brain
47	chr1:78280600-78325600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:78281000-78291600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:78281000-78296600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr1:78281000-78308800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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