Variant report

Variant	rs13140255
Chromosome Location	chr4:120172355-120172356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11722940	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11724619	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11725433	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728178	0.81[ASN][1000 genomes]
rs11729960	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11733606	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734808	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11736997	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11737068	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11737560	0.90[ASN][1000 genomes]
rs13104050	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106878	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13112320	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13113462	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13113662	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13122306	0.81[ASN][1000 genomes]
rs13127517	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13139711	0.83[EUR][1000 genomes]
rs13144426	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397611	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1511021	0.90[ASN][1000 genomes]
rs1511022	0.90[ASN][1000 genomes]
rs17050312	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17334151	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517075	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17517470	0.81[ASN][1000 genomes]
rs17595468	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17595769	0.81[ASN][1000 genomes]
rs17595790	0.81[ASN][1000 genomes]
rs2036859	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34125807	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34156358	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34478210	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34624042	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34733524	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34878806	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34951506	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35137697	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35225855	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35612705	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35646004	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35830965	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35846514	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35917388	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817230	0.81[ASN][1000 genomes]
rs3817242	0.81[ASN][1000 genomes]
rs56818816	0.85[ASN][1000 genomes]
rs62320715	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62320716	0.81[ASN][1000 genomes]
rs62320717	0.81[ASN][1000 genomes]
rs62320718	0.81[ASN][1000 genomes]
rs62320719	0.80[ASN][1000 genomes]
rs62320720	0.81[ASN][1000 genomes]
rs62320721	0.81[ASN][1000 genomes]
rs62320722	0.81[ASN][1000 genomes]
rs62320723	0.81[ASN][1000 genomes]
rs62320724	0.81[ASN][1000 genomes]
rs62320725	0.81[ASN][1000 genomes]
rs62320731	0.81[ASN][1000 genomes]
rs62320732	0.81[ASN][1000 genomes]
rs62320733	0.81[ASN][1000 genomes]
rs62320735	0.81[ASN][1000 genomes]
rs62320737	0.81[ASN][1000 genomes]
rs62326356	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62328380	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328402	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328403	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328404	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62328408	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62328420	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6822097	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6846936	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71610255	0.90[ASN][1000 genomes]
rs71627784	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72918504	0.81[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	nsv916641	chr4:119780023-120777320	Strong transcription Weak 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 target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	esv2763386	chr4:120143861-120186968	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv461632	chr4:120158734-120180790	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv461633	chr4:120158734-120180790	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv595332	chr4:120158734-120180790	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13140255	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs13140255	RP11-33B1.1	cis	Thyroid	GTEx
rs13140255	USP53	cis	Whole Blood	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
6	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
7	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
8	chr4:120143000-120176200	Weak transcription	Esophagus	oesophagus
9	chr4:120146000-120178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:120155400-120176200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:120155400-120176400	Weak transcription	Right Ventricle	heart
13	chr4:120155600-120173800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:120155600-120176400	Weak transcription	Brain Substantia Nigra	brain
15	chr4:120155600-120186000	Weak transcription	Fetal Heart	heart
16	chr4:120157600-120176800	Weak transcription	Primary B cells from cord blood	blood
17	chr4:120159400-120200800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:120159400-120201600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:120159400-120206200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:120159600-120200800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:120159800-120188400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:120160400-120174200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:120160800-120195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:120161000-120173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:120162400-120176600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:120163800-120175600	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:120164000-120176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:120164600-120173000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:120165600-120172400	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr4:120165800-120179400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:120165800-120187000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr4:120166000-120183600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:120166000-120195200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:120166200-120175000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:120166200-120175200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:120166400-120173600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:120166400-120175800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:120166400-120180600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:120166400-120187200	Weak transcription	Fetal Kidney	kidney
40	chr4:120166400-120189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:120166400-120206200	Weak transcription	Small Intestine	intestine
42	chr4:120167000-120182200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:120167000-120184000	Strong transcription	Liver	Liver
44	chr4:120167000-120194400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr4:120167200-120172400	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:120167400-120174600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:120167600-120176600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:120167800-120175200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:120167800-120176200	Weak transcription	Fetal Intestine Small	intestine
50	chr4:120167800-120176200	Weak transcription	Fetal Stomach	stomach

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