Variant report

Variant	rs11859378
Chromosome Location	chr16:12140618-12140619
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11075042	0.93[ASN][1000 genomes]
rs11859105	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11859602	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11859670	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11859801	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11862031	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11863344	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11863772	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11864775	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11865036	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11865132	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11865547	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2257492	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2865105	0.93[ASN][1000 genomes]
rs34321532	0.85[ASN][1000 genomes]
rs34701893	0.85[ASN][1000 genomes]
rs35106911	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826097	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826098	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851006	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851007	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3862465	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs459292	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55719789	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55788618	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55845335	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55933754	0.86[ASN][1000 genomes]
rs55995758	0.85[ASN][1000 genomes]
rs56166842	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56325311	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56363861	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62037727	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62037728	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037734	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62037735	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62037736	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037739	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037740	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037741	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7184186	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7186759	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7192463	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7196418	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7200173	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202235	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7202328	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202330	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7202375	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72784623	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72784632	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044821	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8045202	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051298	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052866	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8057116	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv977110	chr16:12123355-12146787	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11859378	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12099600-12141200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr16:12105200-12142200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr16:12109800-12142200	Weak transcription	Gastric	stomach
4	chr16:12112000-12142200	Weak transcription	NHLF	lung
5	chr16:12112000-12144000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr16:12116200-12141000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr16:12119200-12146400	Weak transcription	Fetal Lung	lung
9	chr16:12119400-12142000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr16:12119600-12148400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr16:12121000-12142200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr16:12121400-12155000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr16:12121600-12142000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr16:12122200-12140800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr16:12122800-12144000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr16:12124400-12156600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr16:12124800-12142000	Weak transcription	Esophagus	oesophagus
18	chr16:12124800-12155000	Weak transcription	NH-A	brain
19	chr16:12126400-12150000	Weak transcription	Small Intestine	intestine
20	chr16:12130000-12142200	Weak transcription	Brain Angular Gyrus	brain
21	chr16:12130000-12153000	Weak transcription	Ovary	ovary
22	chr16:12130200-12142000	Weak transcription	Aorta	Aorta
23	chr16:12131000-12141600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr16:12131000-12142200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr16:12131200-12141000	Weak transcription	GM12878-XiMat	blood
26	chr16:12131200-12142200	Weak transcription	Brain Anterior Caudate	brain
27	chr16:12131200-12142200	Weak transcription	Brain Substantia Nigra	brain
28	chr16:12131200-12142200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr16:12131200-12142200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr16:12131200-12144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr16:12131200-12153000	Weak transcription	Right Atrium	heart
32	chr16:12131200-12156600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr16:12131400-12140800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr16:12131400-12148200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr16:12131400-12150800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr16:12131400-12150800	Weak transcription	HSMMtube	muscle
37	chr16:12131600-12140800	Weak transcription	Left Ventricle	heart
38	chr16:12131600-12154800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr16:12131800-12141000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr16:12132000-12150200	Weak transcription	Osteobl	bone
41	chr16:12132800-12154600	Weak transcription	Hela-S3	cervix
42	chr16:12133000-12147400	Weak transcription	NHDF-Ad	bronchial
43	chr16:12133000-12148200	Weak transcription	Fetal Brain Female	brain
44	chr16:12133000-12152800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr16:12133000-12153600	Weak transcription	Fetal Kidney	kidney
46	chr16:12133800-12156400	Weak transcription	Stomach Mucosa	stomach
47	chr16:12134000-12142200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr16:12134000-12145200	Weak transcription	Placenta	Placenta
49	chr16:12134200-12153000	Weak transcription	HepG2	liver
50	chr16:12135600-12142200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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