Variant report

Variant	rs11714793
Chromosome Location	chr3:52924930-52924931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52900488..52902600-chr3:52922846..52925520,2	MCF-7	breast:
2	chr3:52907507..52909644-chr3:52922284..52925387,3	K562	blood:
3	chr3:52924236..52926036-chr3:53079854..53081517,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11130329	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705797	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11707829	0.93[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708337	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11708390	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712498	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713324	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713376	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11713479	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715498	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11716506	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11716612	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11720233	0.86[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720488	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13060282	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062228	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13067373	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13068194	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13069006	1.00[YRI][hapmap]
rs13076033	1.00[ASN][1000 genomes]
rs13089969	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13095705	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1986656	0.93[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001732	0.85[CEU][hapmap]
rs2336661	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2336665	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34026403	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35230793	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35404467	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35569457	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35651539	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36126605	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3733034	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3733035	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3796352	1.00[ASN][1000 genomes]
rs4608686	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56231111	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61473083	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6762260	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6798472	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299621	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299622	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73839535	0.88[AMR][1000 genomes];0.96[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
rs11714793	TMEM110	cis	multi-tissue	Pritchard
rs11714793	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 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	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:52895800-52925200	Weak transcription	Esophagus	oesophagus
5	chr3:52902200-52925200	Weak transcription	Placenta	Placenta
6	chr3:52908200-52925400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:52908200-52925400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:52908400-52930600	Weak transcription	A549	lung
9	chr3:52908600-52926000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:52909200-52925200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52909600-52925400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:52909800-52925200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:52909800-52925400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:52910000-52929400	Weak transcription	HMEC	breast
15	chr3:52910000-52930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:52910200-52925400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:52910200-52929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:52910200-52930000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:52910200-52930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:52910200-52930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:52910400-52930200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:52910600-52926400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:52913200-52926600	Weak transcription	K562	blood
24	chr3:52913600-52925200	Weak transcription	Adipose Nuclei	Adipose
25	chr3:52916400-52930600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:52916600-52926000	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:52917000-52926000	Weak transcription	Psoas Muscle	Psoas
28	chr3:52918400-52926000	Weak transcription	Small Intestine	intestine
29	chr3:52919200-52930200	Weak transcription	Fetal Kidney	kidney
30	chr3:52919800-52926000	Weak transcription	HSMM	muscle
31	chr3:52920000-52926600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:52920000-52929200	Weak transcription	Dnd41	blood
33	chr3:52920200-52925200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:52920200-52925800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:52920200-52929400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:52920200-52929800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:52920400-52925200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:52920400-52925200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:52920400-52925800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:52920400-52925800	Weak transcription	Left Ventricle	heart
41	chr3:52920400-52926600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:52920400-52930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52920400-52930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:52920400-52930600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:52920600-52925200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:52920600-52925400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:52921000-52925200	Weak transcription	Aorta	Aorta
48	chr3:52921200-52925200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:52921400-52925000	Weak transcription	Primary B cells from cord blood	blood
50	chr3:52921600-52926400	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links