Variant report

Variant	rs11234739
Chromosome Location	chr11:86399945-86399946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10501626	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10898526	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs11234738	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11234741	0.96[ASN][1000 genomes]
rs11234743	0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11234744	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11234745	0.95[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11234746	0.94[ASN][1000 genomes]
rs12574672	0.89[ASN][1000 genomes]
rs12575285	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12789412	0.96[ASN][1000 genomes]
rs17211458	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs17818845	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs17819523	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs17819683	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1945142	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2433412	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2433413	0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs2433414	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2433415	0.83[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4619178	0.95[ASN][1000 genomes]
rs539214	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs543336	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs544199	0.95[ASN][1000 genomes]
rs575273	0.95[ASN][1000 genomes]
rs575468	0.95[ASN][1000 genomes]
rs600242	0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs602498	0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs659301	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs66878934	0.89[ASN][1000 genomes]
rs672266	0.80[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs67655324	0.92[ASN][1000 genomes]
rs72959431	0.81[ASN][1000 genomes]
rs72961766	0.89[ASN][1000 genomes]
rs72961771	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs746491	0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7933920	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7939319	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7948924	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs949348	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11234739	CCDC83	cis	cerebellum	SCAN
rs11234739	C11orf82	cis	parietal	SCAN
rs11234739	ME3	cis	Nerve Tibial	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86384800-86400400	Weak transcription	Gastric	stomach
2	chr11:86385200-86411400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:86386600-86431000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:86388000-86409600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:86390000-86403600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:86393000-86406800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:86393800-86400400	Weak transcription	Pancreas	Pancrea
8	chr11:86397600-86400600	Enhancers	Psoas Muscle	Psoas
9	chr11:86397800-86400200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:86397800-86400200	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr11:86397800-86400600	Enhancers	HSMMtube	muscle
12	chr11:86397800-86400600	Enhancers	NHDF-Ad	bronchial
13	chr11:86397800-86400800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr11:86397800-86400800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr11:86398000-86400000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:86398000-86400000	Enhancers	Colon Smooth Muscle	Colon
17	chr11:86398000-86400200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr11:86398000-86400600	Enhancers	NHLF	lung
19	chr11:86398400-86400200	Enhancers	A549	lung
20	chr11:86398400-86400400	Enhancers	GM12878-XiMat	blood
21	chr11:86398400-86400600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:86398600-86400000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:86398600-86400200	Enhancers	Osteobl	bone
24	chr11:86398800-86405400	Weak transcription	Hela-S3	cervix
25	chr11:86399000-86400200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:86399200-86400600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:86399200-86400600	Enhancers	Stomach Smooth Muscle	stomach
28	chr11:86399200-86400600	Enhancers	NH-A	brain
29	chr11:86399400-86400000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:86399400-86400400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:86399400-86400600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:86399400-86400600	Enhancers	Left Ventricle	heart
33	chr11:86399400-86400600	Enhancers	Ovary	ovary
34	chr11:86399400-86400600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr11:86399400-86400600	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr11:86399600-86400000	Enhancers	Rectal Smooth Muscle	rectum
37	chr11:86399600-86400600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:86399600-86400600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:86399600-86400600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:86399600-86400600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr11:86399600-86400600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:86399600-86400600	Enhancers	Placenta	Placenta
43	chr11:86399600-86400600	Enhancers	HSMM	muscle
44	chr11:86399600-86415800	Weak transcription	Fetal Heart	heart
45	chr11:86399800-86400000	Enhancers	Right Ventricle	heart
46	chr11:86399800-86400200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:86399800-86400600	Enhancers	Aorta	Aorta
48	chr11:86399800-86400600	Enhancers	Brain Cingulate Gyrus	brain
49	chr11:86399800-86400600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr11:86399800-86400600	Enhancers	Esophagus	oesophagus

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