Variant report

Variant	rs13106878
Chromosome Location	chr4:120146383-120146384
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119960403..119963318-chr4:120145478..120148032,2	MCF-7	breast:
2	chr4:120146321..120148170-chr4:120150599..120152803,2	K562	blood:
3	chr4:120134215..120136562-chr4:120145620..120147384,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11725433	0.90[ASN][1000 genomes]
rs11729857	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11733606	0.90[ASN][1000 genomes]
rs11734808	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11737560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13104050	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13113462	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs13113662	0.90[ASN][1000 genomes]
rs13127517	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13140255	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13144426	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs1397611	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1511021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17050312	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17334151	0.90[ASN][1000 genomes]
rs17517075	0.85[ASN][1000 genomes]
rs34156358	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34478210	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34624042	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34951506	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35137697	0.90[ASN][1000 genomes]
rs35612705	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35646004	0.85[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35830965	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326356	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62328380	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62328402	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62328403	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62328404	0.90[ASN][1000 genomes]
rs6846936	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71610255	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655064	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7678138	0.91[EUR][1000 genomes];0.89[ASN][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	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	nsv966480	chr4:120144708-120160847	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13106878	USP53	cis	Whole Blood	GTEx
rs13106878	RP11-33B1.1	cis	Thyroid	GTEx
rs13106878	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120134800-120147000	Weak transcription	Fetal Brain Male	brain
2	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:120135000-120154800	Weak transcription	Primary B cells from cord blood	blood
4	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:120135200-120155000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:120135200-120155000	Weak transcription	Small Intestine	intestine
8	chr4:120135200-120163600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:120135400-120159000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:120135600-120155000	Weak transcription	K562	blood
14	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
15	chr4:120136200-120147400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:120136200-120148000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:120136200-120154400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
19	chr4:120136400-120151600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:120136400-120155000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:120136400-120155000	Weak transcription	Stomach Mucosa	stomach
22	chr4:120136400-120156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:120137000-120151000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:120137400-120155000	Weak transcription	Right Atrium	heart
25	chr4:120137600-120154600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:120138600-120148000	Weak transcription	Pancreas	Pancrea
27	chr4:120138800-120155000	Weak transcription	Fetal Thymus	thymus
28	chr4:120139000-120148400	Weak transcription	Gastric	stomach
29	chr4:120139400-120149200	Weak transcription	Fetal Heart	heart
30	chr4:120139400-120151400	Weak transcription	HepG2	liver
31	chr4:120139400-120151600	Weak transcription	Psoas Muscle	Psoas
32	chr4:120139400-120165800	Weak transcription	Fetal Kidney	kidney
33	chr4:120139600-120151200	Weak transcription	Primary T cells from cord blood	blood
34	chr4:120139600-120151600	Weak transcription	Aorta	Aorta
35	chr4:120139600-120153600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:120140000-120155000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:120140200-120154800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:120140200-120154800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:120140600-120151400	Weak transcription	Left Ventricle	heart
40	chr4:120140600-120151600	Weak transcription	Right Ventricle	heart
41	chr4:120140600-120167400	Weak transcription	Colonic Mucosa	Colon
42	chr4:120140800-120152800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:120140800-120154600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:120140800-120154800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:120140800-120158800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:120141000-120149200	Weak transcription	NHLF	lung
47	chr4:120141000-120151200	Weak transcription	Liver	Liver
48	chr4:120141000-120153800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr4:120141000-120154600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:120141000-120154600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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