Variant report

Variant	rs13139045
Chromosome Location	chr4:120168588-120168589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120131912..120135684-chr4:120163783..120168921,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10006304	0.90[CEU][hapmap]
rs10006877	0.80[CEU][hapmap]
rs10010696	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10022262	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10022508	0.83[CEU][hapmap]
rs10029750	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1011054	0.90[CEU][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs10213342	0.99[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11098496	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11098499	0.90[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs11098506	0.90[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs11726229	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs11729897	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11734519	0.99[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11931312	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11944880	1.00[ASW][hapmap];0.90[CEU][hapmap];0.81[CHD][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12186259	0.84[CEU][hapmap]
rs12499598	0.82[EUR][1000 genomes]
rs12501610	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12506395	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12509054	0.85[CEU][hapmap]
rs12512517	0.85[EUR][1000 genomes]
rs13113112	0.90[CEU][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs13114751	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13116504	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13129661	0.89[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13133044	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13435802	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1397608	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1511015	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1511018	0.90[CEU][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs1511019	0.90[CEU][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs1546502	0.80[CEU][hapmap]
rs1546505	0.80[CEU][hapmap];0.86[TSI][hapmap]
rs1551	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17839089	0.82[CEU][hapmap]
rs1814814	0.80[EUR][1000 genomes]
rs28374891	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs28419773	0.83[EUR][1000 genomes]
rs28555550	0.83[EUR][1000 genomes]
rs34585914	0.85[EUR][1000 genomes]
rs34616304	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34630083	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35197422	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35271032	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35434465	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35643470	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35916640	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3749591	0.90[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4145951	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4145952	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56386062	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67073020	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6814412	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6815725	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6824111	0.90[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6832670	0.85[CEU][hapmap]
rs6837898	0.90[CEU][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs6849889	0.90[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7659194	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs7684942	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7685268	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9995136	0.90[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs9995277	0.85[CEU][hapmap]
rs9999724	0.81[TSI][hapmap]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs13139045	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs13139045	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs13139045	RP11-33B1.1	cis	Whole Blood	GTEx
rs13139045	RP11-384K6.6	cis	Whole Blood	GTEx
rs13139045	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs13139045	RP11-33B1.1	cis	lung	GTEx
rs13139045	QRFPR	cis	parietal	SCAN
rs13139045	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs13139045	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs13139045	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
8	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
9	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
10	chr4:120143000-120176200	Weak transcription	Esophagus	oesophagus
11	chr4:120146000-120178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:120155400-120169800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:120155400-120169800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:120155400-120169800	Weak transcription	Ovary	ovary
16	chr4:120155400-120176200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:120155400-120176400	Weak transcription	Right Ventricle	heart
18	chr4:120155600-120169800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:120155600-120173800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:120155600-120176400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:120155600-120186000	Weak transcription	Fetal Heart	heart
22	chr4:120157000-120170000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:120157600-120176800	Weak transcription	Primary B cells from cord blood	blood
24	chr4:120159400-120200800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:120159400-120201600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:120159400-120206200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:120159600-120170000	Weak transcription	K562	blood
28	chr4:120159600-120200800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:120159800-120188400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:120160400-120174200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:120160800-120195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:120161000-120173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:120161600-120170000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:120162400-120176600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:120163800-120169800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:120163800-120175600	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:120164000-120176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr4:120164600-120173000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:120165000-120171400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:120165600-120172400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr4:120165800-120172000	Strong transcription	NHDF-Ad	bronchial
42	chr4:120165800-120179400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:120165800-120187000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr4:120166000-120168800	Strong transcription	HMEC	breast
45	chr4:120166000-120183600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:120166000-120195200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:120166200-120170000	Weak transcription	Stomach Mucosa	stomach
48	chr4:120166200-120170600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:120166200-120171400	Strong transcription	Osteobl	bone
50	chr4:120166200-120172000	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links