Variant report

Variant	rs7543125
Chromosome Location	chr1:78283714-78283715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1038983	0.84[EUR][1000 genomes]
rs10873954	0.96[ASN][1000 genomes]
rs10873955	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162380	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11162383	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162384	1.00[ASN][1000 genomes]
rs11162386	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162387	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578805	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1166584	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1166586	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1166589	0.97[ASN][1000 genomes]
rs12026939	0.84[EUR][1000 genomes]
rs12090729	1.00[ASN][1000 genomes]
rs12132838	0.84[ASN][1000 genomes]
rs12142441	0.86[ASN][1000 genomes]
rs1539739	1.00[ASN][1000 genomes]
rs1977900	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2031342	0.86[ASN][1000 genomes]
rs2147318	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs278833	0.87[EUR][1000 genomes]
rs278836	0.84[EUR][1000 genomes]
rs278843	0.87[EUR][1000 genomes]
rs278857	0.85[EUR][1000 genomes]
rs278858	0.85[EUR][1000 genomes]
rs278859	0.87[EUR][1000 genomes]
rs278864	0.87[EUR][1000 genomes]
rs366467	0.83[EUR][1000 genomes]
rs370335	0.84[EUR][1000 genomes]
rs3767038	0.84[ASN][1000 genomes]
rs4488068	0.86[ASN][1000 genomes]
rs4949661	0.81[EUR][1000 genomes]
rs4949822	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56688304	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6603956	0.84[EUR][1000 genomes]
rs6657290	0.84[EUR][1000 genomes]
rs6670660	0.81[EUR][1000 genomes]
rs6672200	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6674638	0.83[EUR][1000 genomes]
rs6687596	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6691317	0.80[EUR][1000 genomes]
rs6698151	0.81[EUR][1000 genomes]
rs717333	0.84[ASN][1000 genomes]
rs7519946	0.84[ASN][1000 genomes]
rs7535781	0.84[ASN][1000 genomes]
rs7536206	1.00[ASN][1000 genomes]
rs7543037	1.00[ASN][1000 genomes]
rs7545175	0.81[EUR][1000 genomes]
rs7556227	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8179272	0.97[ASN][1000 genomes]
rs9662527	0.87[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
rs7543125	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	chr1:78246000-78284200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:78246000-78285600	Weak transcription	Colonic Mucosa	Colon
3	chr1:78246400-78287400	Weak transcription	Fetal Heart	heart
4	chr1:78248600-78288200	Weak transcription	Small Intestine	intestine
5	chr1:78252200-78315800	Weak transcription	Esophagus	oesophagus
6	chr1:78253000-78283800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:78254400-78287200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:78262800-78285200	Weak transcription	Gastric	stomach
9	chr1:78266000-78298000	Weak transcription	K562	blood
10	chr1:78266200-78299200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:78266200-78299200	Weak transcription	Pancreas	Pancrea
12	chr1:78266600-78284200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:78268400-78291200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:78272400-78286200	Weak transcription	Stomach Mucosa	stomach
15	chr1:78273400-78289600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:78273600-78290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:78273600-78290000	Weak transcription	Psoas Muscle	Psoas
18	chr1:78273600-78293200	Weak transcription	Brain Germinal Matrix	brain
19	chr1:78273800-78284000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:78273800-78284200	Weak transcription	Spleen	Spleen
21	chr1:78274600-78288600	Weak transcription	HepG2	liver
22	chr1:78274600-78290800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:78274800-78284000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:78274800-78297400	Weak transcription	Brain Substantia Nigra	brain
25	chr1:78274800-78297600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:78274800-78298000	Weak transcription	Fetal Kidney	kidney
27	chr1:78275000-78284000	Weak transcription	Ovary	ovary
28	chr1:78275000-78289000	Weak transcription	A549	lung
29	chr1:78275000-78312800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:78277000-78290200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:78277400-78291200	Strong transcription	Fetal Intestine Small	intestine
32	chr1:78277600-78292600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr1:78278400-78284400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:78278400-78286200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:78278400-78286400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:78278400-78289600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:78278600-78286400	Strong transcription	Primary T cells from cord blood	blood
38	chr1:78278600-78287000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:78278800-78287400	Strong transcription	Placenta	Placenta
40	chr1:78278800-78288800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:78278800-78290200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:78279200-78286600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:78279200-78288000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:78279200-78288000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:78279200-78288200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:78279200-78288200	Strong transcription	Liver	Liver
47	chr1:78279200-78288400	Strong transcription	Fetal Intestine Large	intestine
48	chr1:78279200-78288800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:78279200-78289600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:78279200-78300400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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