Variant report

Variant	rs34872575
Chromosome Location	chr3:52986277-52986278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10510761	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705797	0.89[ASN][1000 genomes]
rs11706035	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707575	0.84[EUR][1000 genomes]
rs11707780	0.89[EUR][1000 genomes]
rs11708337	0.89[ASN][1000 genomes]
rs11710292	0.84[EUR][1000 genomes]
rs11710394	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11710707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711773	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11712653	0.89[EUR][1000 genomes]
rs11713171	0.89[EUR][1000 genomes]
rs11713206	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713290	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713376	0.89[ASN][1000 genomes]
rs11713859	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11714037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714876	0.84[EUR][1000 genomes]
rs11714902	0.84[EUR][1000 genomes]
rs11715231	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715498	0.89[ASN][1000 genomes]
rs11716506	0.89[ASN][1000 genomes]
rs11716612	0.89[ASN][1000 genomes]
rs11717132	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717619	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717715	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718388	0.89[EUR][1000 genomes]
rs11718538	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718752	0.84[EUR][1000 genomes]
rs11718834	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720191	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11720488	0.89[ASN][1000 genomes]
rs13058817	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13062228	0.89[ASN][1000 genomes]
rs13067373	0.89[ASN][1000 genomes]
rs13068194	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13069006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072395	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072457	0.84[EUR][1000 genomes]
rs13072818	0.89[EUR][1000 genomes]
rs13074524	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13078971	0.84[EUR][1000 genomes]
rs13084937	0.84[EUR][1000 genomes]
rs13085514	0.84[EUR][1000 genomes]
rs13085544	0.81[EUR][1000 genomes]
rs13089969	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13091844	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13092352	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095705	0.89[ASN][1000 genomes]
rs13320044	0.84[EUR][1000 genomes]
rs1346719	0.89[EUR][1000 genomes]
rs17052727	0.89[EUR][1000 genomes]
rs2336540	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336541	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2564926	0.82[EUR][1000 genomes]
rs2581807	0.82[EUR][1000 genomes]
rs3097417	0.82[EUR][1000 genomes]
rs34121720	0.89[EUR][1000 genomes]
rs34238610	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34244302	0.84[EUR][1000 genomes]
rs34313969	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34340609	0.89[EUR][1000 genomes]
rs34493168	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34933390	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34943350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34979715	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35076015	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35163227	0.84[EUR][1000 genomes]
rs35174175	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35230793	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35378159	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384050	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35385050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35404467	0.89[ASN][1000 genomes]
rs35507120	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35569457	0.89[ASN][1000 genomes]
rs35720014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35737577	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35849389	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36090694	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36126605	0.89[ASN][1000 genomes]
rs3733034	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3733035	0.89[ASN][1000 genomes]
rs3796352	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3806692	0.89[EUR][1000 genomes]
rs3821872	0.89[EUR][1000 genomes]
rs4478072	0.84[EUR][1000 genomes]
rs4608686	0.82[ASN][1000 genomes]
rs56231111	0.89[ASN][1000 genomes]
rs58515094	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58660500	0.89[EUR][1000 genomes]
rs59583591	0.84[EUR][1000 genomes]
rs60887045	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60942590	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61172708	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61473083	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6445555	0.81[EUR][1000 genomes]
rs6445556	0.87[EUR][1000 genomes]
rs6445557	0.87[EUR][1000 genomes]
rs6762260	0.89[ASN][1000 genomes]
rs71299622	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71299700	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71301804	0.87[EUR][1000 genomes]
rs71301808	0.89[EUR][1000 genomes]
rs71301809	0.84[EUR][1000 genomes]
rs71301811	0.82[EUR][1000 genomes]
rs71301814	0.84[EUR][1000 genomes]
rs71617204	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73839535	0.89[ASN][1000 genomes]
rs750474	0.87[EUR][1000 genomes]
rs7622420	0.84[EUR][1000 genomes]
rs7625448	0.84[EUR][1000 genomes]
rs7640293	0.84[EUR][1000 genomes]
rs7645611	0.84[EUR][1000 genomes]
rs9756317	0.82[EUR][1000 genomes]
rs9875573	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	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
2	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
3	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34872575	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
2	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
3	chr3:52955200-52986400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:52956400-52986400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:52961600-52987000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:52962400-52986600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:52962400-52998200	Weak transcription	Lung	lung
8	chr3:52962400-53001600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:52962400-53007000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
11	chr3:52964200-52995400	Weak transcription	Gastric	stomach
12	chr3:52964400-52988200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:52965000-52986800	Weak transcription	Thymus	Thymus
15	chr3:52965000-52998400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
17	chr3:52965200-52986600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood
19	chr3:52966400-53001600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:52968800-52986400	Weak transcription	Fetal Thymus	thymus
21	chr3:52969000-52986400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:52969000-53008000	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:52969200-52986400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:52969200-52991000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:52969200-52996200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:52969200-52997400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:52969400-52986600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:52972400-52986400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:52975000-53008000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:52975200-52986400	Weak transcription	Primary T cells from cord blood	blood
31	chr3:52975200-53000600	Weak transcription	Hela-S3	cervix
32	chr3:52976400-52986400	Weak transcription	Primary B cells from cord blood	blood
33	chr3:52977000-52987000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:52977600-52986400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:52977600-52986400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:52977600-53017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:52980400-52996600	Weak transcription	Psoas Muscle	Psoas
38	chr3:52980800-52990000	Weak transcription	Brain Anterior Caudate	brain
39	chr3:52983600-52988200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:52983800-52986400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:52984000-52986400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:52984000-52998800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:52984400-52988200	Strong transcription	Fetal Stomach	stomach
44	chr3:52984400-53006000	Weak transcription	Fetal Heart	heart
45	chr3:52984600-53003000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:52985000-52988000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:52985200-52988400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:52985600-52987400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:52985800-52987000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:52985800-52987600	Strong transcription	Primary T cells fromperipheralblood	blood

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