Variant report

Variant	rs9754878
Chromosome Location	chr3:48897595-48897596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10780033	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130176	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1134591	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11705737	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11705888	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11708022	0.92[ASN][1000 genomes]
rs11709246	0.92[ASN][1000 genomes]
rs11712982	0.90[ASN][1000 genomes]
rs11713694	0.95[ASN][1000 genomes]
rs11717978	0.92[ASN][1000 genomes]
rs11719457	0.92[ASN][1000 genomes]
rs11920534	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11924597	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12491743	0.80[EUR][1000 genomes]
rs12493289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637037	0.86[EUR][1000 genomes]
rs13064883	0.93[EUR][1000 genomes]
rs13064911	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072911	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13073997	0.97[ASN][1000 genomes]
rs13076394	0.94[EUR][1000 genomes]
rs13078308	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13086240	0.90[ASN][1000 genomes]
rs13087930	0.92[ASN][1000 genomes]
rs13090839	0.90[ASN][1000 genomes]
rs13094900	0.95[ASN][1000 genomes]
rs13315711	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13316620	0.87[EUR][1000 genomes]
rs28642807	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34037363	0.82[ASN][1000 genomes]
rs34477108	0.92[ASN][1000 genomes]
rs34504524	0.85[ASN][1000 genomes]
rs34509487	0.92[ASN][1000 genomes]
rs3774628	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4072859	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4974078	0.81[ASN][1000 genomes]
rs4974079	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974080	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4974082	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4974084	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974085	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974087	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974091	0.87[EUR][1000 genomes]
rs55674449	0.85[ASN][1000 genomes]
rs56318350	0.92[ASN][1000 genomes]
rs6414613	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442130	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6446196	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446198	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446205	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6446252	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6446253	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67060340	0.97[ASN][1000 genomes]
rs67332931	0.92[ASN][1000 genomes]
rs6768433	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6781790	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6786665	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6789285	0.88[EUR][1000 genomes]
rs6791234	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6791542	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6795025	0.86[EUR][1000 genomes]
rs71324924	0.92[ASN][1000 genomes]
rs7372149	0.86[EUR][1000 genomes]
rs7373778	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7373790	0.85[EUR][1000 genomes]
rs7430198	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7430501	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7431710	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431857	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7432989	0.82[EUR][1000 genomes]
rs7612459	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7615235	0.83[EUR][1000 genomes]
rs7615675	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7616815	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7621015	0.90[EUR][1000 genomes]
rs7623023	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7626445	0.83[EUR][1000 genomes]
rs7627404	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7628719	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7630742	0.83[EUR][1000 genomes]
rs7636057	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7639332	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7643368	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7647093	0.88[EUR][1000 genomes]
rs7649458	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7653459	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8926	0.87[EUR][1000 genomes]
rs9311430	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9311432	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9311433	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9311434	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9681717	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9682444	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9755490	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830636	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9835307	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840684	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9846123	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9850134	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867373	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9876848	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9879971	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9884022	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][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	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	esv3412312	chr3:48895048-48897746	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs9754878	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs9754878	WDR6	cis	Adipose Subcutaneous	GTEx
rs9754878	WDR6	cis	Muscle Skeletal	GTEx
rs9754878	AMT	cis	Thyroid	GTEx
rs9754878	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9754878	WDR6	cis	Esophagus Muscularis	GTEx
rs9754878	CCDC36	cis	Artery Tibial	GTEx
rs9754878	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs9754878	NICN1	cis	Thyroid	GTEx
rs9754878	WDR6	cis	Whole Blood	GTEx
rs9754878	NCKIPSD	cis	Whole Blood	GTEx
rs9754878	WDR6	cis	Nerve Tibial	GTEx
rs9754878	NCKIPSD	cis	Nerve Tibial	GTEx
rs9754878	AMT	cis	Whole Blood	GTEx
rs9754878	AMT	cis	Muscle Skeletal	GTEx
rs9754878	ARIH2	cis	Thyroid	GTEx
rs9754878	WDR6	cis	lung	GTEx
rs9754878	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs9754878	NCKIPSD	cis	Muscle Skeletal	GTEx
rs9754878	AMT	cis	Artery Aorta	GTEx
rs9754878	WDR6	cis	Artery Tibial	GTEx
rs9754878	WDR6	cis	Esophagus Mucosa	GTEx
rs9754878	NICN1-AS1	cis	Thyroid	GTEx
rs9754878	WDR6	cis	Heart Left Ventricle	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48885600-48915000	Weak transcription	Small Intestine	intestine
2	chr3:48885800-48899600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:48885800-48900600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:48885800-48906600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:48885800-48913600	Weak transcription	Fetal Lung	lung
6	chr3:48886000-48897800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:48886000-48899000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:48886000-48899600	Weak transcription	NHEK	skin
9	chr3:48886000-48899800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:48886200-48900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:48886200-48900400	Weak transcription	NHLF	lung
12	chr3:48886200-48900800	Weak transcription	NHDF-Ad	bronchial
13	chr3:48886400-48897800	Weak transcription	Osteobl	bone
14	chr3:48886400-48899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:48886600-48901800	Weak transcription	Fetal Heart	heart
16	chr3:48889200-48902000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:48889400-48901200	Weak transcription	Fetal Brain Male	brain
18	chr3:48889600-48935400	Weak transcription	Brain Germinal Matrix	brain
19	chr3:48889800-48916800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:48891600-48904600	Weak transcription	HSMM	muscle
21	chr3:48892600-48897600	Strong transcription	Liver	Liver
22	chr3:48893200-48900400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr3:48893200-48900600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:48893400-48897600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:48893400-48900200	Strong transcription	Fetal Thymus	thymus
26	chr3:48893800-48897600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:48893800-48897600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:48893800-48900200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:48893800-48900600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:48894000-48897600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:48894200-48900400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:48894400-48902200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:48894400-48923000	Strong transcription	Fetal Intestine Small	intestine
34	chr3:48894600-48918800	Weak transcription	HepG2	liver
35	chr3:48894800-48899600	Weak transcription	Brain Angular Gyrus	brain
36	chr3:48895800-48900800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:48896000-48897600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:48896400-48934400	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:48896600-48899200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:48896600-48918600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:48896800-48899200	Weak transcription	Placenta	Placenta
42	chr3:48896800-48899600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:48896800-48900200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:48896800-48934200	Weak transcription	Stomach Mucosa	stomach
45	chr3:48896800-48935000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:48897000-48898400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:48897000-48898600	Weak transcription	Pancreas	Pancrea
48	chr3:48897000-48898600	Weak transcription	Right Ventricle	heart
49	chr3:48897000-48899400	Weak transcription	Primary T cells from cord blood	blood
50	chr3:48897000-48899400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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