Variant report

Variant	rs11713479
Chromosome Location	chr3:52927060-52927061
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	chr3:52925161..52929038-chr3:52929982..52933172,4	MCF-7	breast:
2	chr3:52925648..52928191-chr3:52930062..52932793,2	K562	blood:

Variant related genes	Relation type
ENSG00000213533	Chromatin interaction
ENSG00000248592	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10510761	0.82[AFR][1000 genomes]
rs11130329	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11705797	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11707829	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11708337	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11708390	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11710394	0.84[AFR][1000 genomes]
rs11712498	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11713290	0.88[AFR][1000 genomes]
rs11713324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11713376	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11714793	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715498	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11716506	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11716612	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11717132	0.88[AFR][1000 genomes]
rs11718538	0.88[AFR][1000 genomes]
rs11718834	0.88[AFR][1000 genomes]
rs11720191	0.84[AFR][1000 genomes]
rs11720233	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11720488	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13060282	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13062228	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13067373	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13068194	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13074524	0.82[AFR][1000 genomes]
rs13076033	0.90[ASN][1000 genomes]
rs13089969	0.90[ASN][1000 genomes]
rs13092352	0.88[AFR][1000 genomes]
rs13095705	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1986656	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2336540	0.88[AFR][1000 genomes]
rs2336541	0.84[AFR][1000 genomes]
rs2336661	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2336665	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34026403	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34313969	0.88[AFR][1000 genomes]
rs35230793	0.90[ASN][1000 genomes]
rs35384050	0.84[AFR][1000 genomes]
rs35404467	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35569457	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35651539	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35737577	0.82[AFR][1000 genomes]
rs35849389	0.84[AFR][1000 genomes]
rs36126605	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733034	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3733035	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3796352	0.90[ASN][1000 genomes]
rs4608686	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56231111	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58515094	0.88[AFR][1000 genomes]
rs60887045	0.88[AFR][1000 genomes]
rs60942590	0.84[AFR][1000 genomes]
rs61172708	0.88[AFR][1000 genomes]
rs61473083	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6762260	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6798472	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71299621	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71299622	0.90[ASN][1000 genomes]
rs73839535	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11713479	TMEM110	cis	multi-tissue	Pritchard
rs11713479	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
2	chr3:52908400-52930600	Weak transcription	A549	lung
3	chr3:52910000-52929400	Weak transcription	HMEC	breast
4	chr3:52910000-52930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52910200-52929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:52910200-52930000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:52910200-52930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:52910200-52930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:52910400-52930200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:52916400-52930600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:52919200-52930200	Weak transcription	Fetal Kidney	kidney
12	chr3:52920000-52929200	Weak transcription	Dnd41	blood
13	chr3:52920200-52929400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:52920200-52929800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:52920400-52930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:52920400-52930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:52920400-52930600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:52921600-52930600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:52921800-52927800	Weak transcription	Right Ventricle	heart
20	chr3:52923400-52927400	Enhancers	Fetal Lung	lung
21	chr3:52923800-52928800	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:52924000-52927200	Enhancers	Pancreas	Pancrea
23	chr3:52924000-52929400	Enhancers	Brain Hippocampus Middle	brain
24	chr3:52924000-52930000	Enhancers	Brain Substantia Nigra	brain
25	chr3:52924200-52927200	Enhancers	Gastric	stomach
26	chr3:52924200-52930200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr3:52924400-52928400	Enhancers	Stomach Mucosa	stomach
28	chr3:52924600-52930200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr3:52924800-52929600	Genic enhancers	Thymus	Thymus
30	chr3:52925000-52927800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:52925000-52928200	Weak transcription	Fetal Brain Female	brain
32	chr3:52925000-52928800	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr3:52925200-52928000	Enhancers	Primary B cells from peripheral blood	blood
34	chr3:52925200-52928200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr3:52925200-52928200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:52925200-52928400	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:52925200-52928400	Flanking Active TSS	GM12878-XiMat	blood
38	chr3:52925200-52928800	Enhancers	Adipose Nuclei	Adipose
39	chr3:52925200-52929600	Genic enhancers	Fetal Thymus	thymus
40	chr3:52925400-52927600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:52925400-52928200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:52925400-52928400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:52925400-52929800	Enhancers	Brain Anterior Caudate	brain
44	chr3:52925400-52929800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:52925400-52929800	Weak transcription	NHEK	skin
46	chr3:52925600-52928200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:52925600-52928200	Enhancers	Fetal Intestine Small	intestine
48	chr3:52925600-52928800	Weak transcription	Brain Germinal Matrix	brain
49	chr3:52925600-52930200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:52925600-52930600	Weak transcription	Esophagus	oesophagus

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