Variant report

Variant	rs13089969
Chromosome Location	chr3:52918267-52918268
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10510761	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130329	1.00[ASN][1000 genomes]
rs11706035	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11707829	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11708390	1.00[ASN][1000 genomes]
rs11710394	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11710707	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11711773	0.82[EUR][1000 genomes]
rs11712498	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11713206	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11713290	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11713324	1.00[ASN][1000 genomes]
rs11713479	0.90[ASN][1000 genomes]
rs11713859	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11714037	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11714793	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11715231	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11717132	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11717619	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11717715	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11718538	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11718834	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11720191	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11720233	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13058817	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13060282	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13069006	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13072395	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13074524	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13076033	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13078834	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13091844	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13092352	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1986656	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2336540	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2336541	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2336661	0.95[ASN][1000 genomes]
rs2336665	1.00[ASN][1000 genomes]
rs34026403	1.00[ASN][1000 genomes]
rs34238610	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34313969	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34493168	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34872575	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34933390	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34943350	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34979715	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35076015	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35174175	0.84[EUR][1000 genomes]
rs35230793	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35378159	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35384050	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35385050	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35507120	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35651539	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35720014	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35737577	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35849389	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36090694	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3796352	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58515094	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60887045	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60942590	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61172708	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6798472	1.00[ASN][1000 genomes]
rs71299621	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71299622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71299700	0.81[EUR][1000 genomes]
rs71617204	0.81[AMR][1000 genomes];0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13089969	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
3	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
4	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
7	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:52895400-52919400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:52895800-52923800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:52895800-52925200	Weak transcription	Esophagus	oesophagus
11	chr3:52902200-52925200	Weak transcription	Placenta	Placenta
12	chr3:52904000-52918400	Weak transcription	Fetal Intestine Large	intestine
13	chr3:52904600-52919400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:52905000-52919800	Weak transcription	Right Ventricle	heart
15	chr3:52906000-52924400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:52908000-52924000	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:52908000-52924000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:52908200-52919000	Weak transcription	NHEK	skin
19	chr3:52908200-52919600	Weak transcription	HSMM	muscle
20	chr3:52908200-52925400	Weak transcription	Brain Anterior Caudate	brain
21	chr3:52908200-52925400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:52908400-52924400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:52908400-52924600	Weak transcription	NHLF	lung
24	chr3:52908400-52930600	Weak transcription	A549	lung
25	chr3:52908600-52924600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:52908600-52926000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:52909200-52919400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:52909200-52920000	Weak transcription	Liver	Liver
29	chr3:52909200-52925200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:52909600-52925400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:52909800-52925200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:52909800-52925400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:52910000-52918800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:52910000-52919400	Weak transcription	Dnd41	blood
35	chr3:52910000-52929400	Weak transcription	HMEC	breast
36	chr3:52910000-52930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:52910200-52920200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:52910200-52925400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:52910200-52929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:52910200-52930000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:52910200-52930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:52910200-52930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:52910400-52920200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:52910400-52924800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:52910400-52930200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:52910600-52926400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:52911600-52921400	Weak transcription	Spleen	Spleen
48	chr3:52912200-52918800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:52912400-52919600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:52913000-52919600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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