Variant report

Variant	rs1511016
Chromosome Location	chr4:120170355-120170356
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119991797..119993940-chr4:120168867..120171491,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10000726	0.82[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10006850	0.80[ASN][1000 genomes]
rs10010174	0.82[ASN][1000 genomes]
rs10034579	0.81[TSI][hapmap]
rs10034661	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs1011052	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10857065	0.84[ASN][1000 genomes]
rs11737086	0.89[CEU][hapmap]
rs1397610	0.89[CEU][hapmap]
rs1397613	0.81[TSI][hapmap]
rs1799883	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs2282688	0.81[TSI][hapmap]
rs4496567	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834765	0.82[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4834770	0.81[TSI][hapmap]
rs6534131	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6823331	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833072	0.88[CEU][hapmap]
rs6841872	0.94[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs7356185	0.82[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs7656644	0.81[CHB][hapmap]
rs7676969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681373	0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs953966	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[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
rs1511016	RP11-33B1.1	cis	Muscle Skeletal	GTEx
rs1511016	USP53	cis	parietal	SCAN
rs1511016	RP11-33B1.1	cis	Nerve Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
7	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
8	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
9	chr4:120143000-120176200	Weak transcription	Esophagus	oesophagus
10	chr4:120146000-120178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:120155400-120176200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:120155400-120176400	Weak transcription	Right Ventricle	heart
14	chr4:120155600-120173800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:120155600-120176400	Weak transcription	Brain Substantia Nigra	brain
16	chr4:120155600-120186000	Weak transcription	Fetal Heart	heart
17	chr4:120157600-120176800	Weak transcription	Primary B cells from cord blood	blood
18	chr4:120159400-120200800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:120159400-120201600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:120159400-120206200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:120159600-120200800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:120159800-120188400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:120160400-120174200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:120160800-120195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:120161000-120173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:120162400-120176600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:120163800-120175600	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:120164000-120176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:120164600-120173000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:120165000-120171400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:120165600-120172400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr4:120165800-120172000	Strong transcription	NHDF-Ad	bronchial
33	chr4:120165800-120179400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:120165800-120187000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:120166000-120183600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:120166000-120195200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:120166200-120170600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:120166200-120171400	Strong transcription	Osteobl	bone
39	chr4:120166200-120172000	Weak transcription	Brain Germinal Matrix	brain
40	chr4:120166200-120175000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr4:120166200-120175200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:120166400-120173600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:120166400-120175800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:120166400-120180600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:120166400-120187200	Weak transcription	Fetal Kidney	kidney
46	chr4:120166400-120189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:120166400-120206200	Weak transcription	Small Intestine	intestine
48	chr4:120166600-120172000	Strong transcription	HSMM	muscle
49	chr4:120166600-120172000	Strong transcription	HUVEC	blood vessel
50	chr4:120167000-120170600	Strong transcription	Primary T cells from cord blood	blood

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