Variant report

Variant	rs11679928
Chromosome Location	chr2:114042456-114042457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10201645	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10209795	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11123174	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11123175	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11683025	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11687706	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11688620	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11889663	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12467534	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12989922	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13002606	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13022812	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13385108	0.85[AMR][1000 genomes]
rs13388160	0.87[AMR][1000 genomes]
rs17626434	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17626470	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34657362	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4091938	0.85[AMR][1000 genomes]
rs4848324	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4848325	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4848326	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4848327	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4848328	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4848329	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4848330	0.83[AMR][1000 genomes]
rs4849191	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4849192	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4849194	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6753679	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6760462	0.85[AMR][1000 genomes]
rs7587376	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv961872	chr2:114041837-114061641	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11679928	PAX8	cis	lung	GTEx
rs11679928	AC016683.6	cis	Whole Blood	GTEx
rs11679928	AC016683.6	cis	Muscle Skeletal	GTEx
rs11679928	AC016683.6	cis	lung	GTEx
rs11679928	AC016683.6	cis	Nerve Tibial	GTEx
rs11679928	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs11679928	PAX8	cis	Esophagus Muscularis	GTEx
rs11679928	PAX8	cis	Adipose Subcutaneous	GTEx
rs11679928	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs11679928	AC016683.6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114036600-114043800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:114037400-114043600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:114037600-114043800	Enhancers	HMEC	breast
4	chr2:114038200-114043800	Enhancers	Fetal Intestine Large	intestine
5	chr2:114038400-114043600	Enhancers	Fetal Intestine Small	intestine
6	chr2:114038600-114043600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:114038600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:114039000-114043800	Enhancers	HSMM	muscle
9	chr2:114039400-114043000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:114039400-114043200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:114039400-114043200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr2:114039600-114042600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:114039600-114043400	Enhancers	Osteobl	bone
14	chr2:114039600-114043600	Enhancers	HSMMtube	muscle
15	chr2:114039600-114043800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:114039800-114043600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:114040000-114042600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:114040200-114042600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:114040400-114042800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:114040600-114043600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:114040600-114043600	Enhancers	Colon Smooth Muscle	Colon
22	chr2:114040600-114043600	Enhancers	NHDF-Ad	bronchial
23	chr2:114040600-114047000	Enhancers	Liver	Liver
24	chr2:114040600-114047800	Weak transcription	Gastric	stomach
25	chr2:114040800-114043400	Enhancers	NHLF	lung
26	chr2:114041000-114042600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr2:114041000-114043600	Enhancers	Rectal Smooth Muscle	rectum
28	chr2:114041200-114042800	Enhancers	Fetal Stomach	stomach
29	chr2:114041200-114043600	Enhancers	NHEK	skin
30	chr2:114041400-114042600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:114041400-114042800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:114041400-114043800	Enhancers	A549	lung
33	chr2:114041600-114042600	Enhancers	Spleen	Spleen
34	chr2:114041600-114042600	Enhancers	HepG2	liver
35	chr2:114041600-114043400	Enhancers	Lung	lung
36	chr2:114041600-114043600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr2:114041800-114042600	Enhancers	Fetal Kidney	kidney
38	chr2:114041800-114042600	Enhancers	Ovary	ovary
39	chr2:114041800-114042800	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr2:114042200-114043200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:114042200-114043400	Weak transcription	Pancreas	Pancrea
42	chr2:114042200-114044200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:114042200-114045400	Weak transcription	Stomach Mucosa	stomach
44	chr2:114042200-114046000	Weak transcription	Brain Anterior Caudate	brain
45	chr2:114042200-114046200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:114042400-114042600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:114042400-114043600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr2:114042400-114043600	Enhancers	NH-A	brain
49	chr2:114042400-114044600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:114042400-114045000	Weak transcription	Brain Inferior Temporal Lobe	brain

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