Variant report

Variant	rs12246008
Chromosome Location	chr10:116761769-116761770
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10160015	0.90[ASN][1000 genomes]
rs10444099	0.95[ASN][1000 genomes]
rs1045657	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510008	0.81[ASN][1000 genomes]
rs10885632	0.81[ASN][1000 genomes]
rs10885633	0.95[ASN][1000 genomes]
rs10885634	0.95[ASN][1000 genomes]
rs10885636	0.95[ASN][1000 genomes]
rs10885637	0.95[ASN][1000 genomes]
rs10885638	0.95[ASN][1000 genomes]
rs10885639	0.95[ASN][1000 genomes]
rs11196983	0.81[ASN][1000 genomes]
rs11196984	0.81[ASN][1000 genomes]
rs11196989	0.81[ASN][1000 genomes]
rs11196991	0.95[ASN][1000 genomes]
rs11196996	0.95[ASN][1000 genomes]
rs11196999	0.95[ASN][1000 genomes]
rs11197000	0.95[ASN][1000 genomes]
rs11197005	0.95[ASN][1000 genomes]
rs11197006	0.87[ASN][1000 genomes]
rs11197007	0.95[ASN][1000 genomes]
rs11197010	0.95[ASN][1000 genomes]
rs11197011	0.95[ASN][1000 genomes]
rs11197012	0.95[ASN][1000 genomes]
rs11197023	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098332	1.00[ASN][1000 genomes]
rs12265048	0.81[ASN][1000 genomes]
rs12269261	0.95[ASN][1000 genomes]
rs12764662	1.00[ASN][1000 genomes]
rs12772737	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774597	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12779231	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092671	0.92[EUR][1000 genomes]
rs17721905	1.00[ASN][1000 genomes]
rs17722042	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795104	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795212	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095379	0.95[ASN][1000 genomes]
rs2105001	0.95[ASN][1000 genomes]
rs2420070	0.81[ASN][1000 genomes]
rs34170154	1.00[ASN][1000 genomes]
rs34200762	0.89[EUR][1000 genomes]
rs34318200	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34434610	1.00[ASN][1000 genomes]
rs34453431	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34461950	0.91[ASN][1000 genomes]
rs35501899	1.00[ASN][1000 genomes]
rs35811923	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3931556	0.95[ASN][1000 genomes]
rs61869271	1.00[ASN][1000 genomes]
rs61869272	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869274	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869275	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869297	0.80[EUR][1000 genomes]
rs6585302	0.81[ASN][1000 genomes]
rs6585306	0.95[ASN][1000 genomes]
rs6585309	1.00[ASN][1000 genomes]
rs6585310	1.00[ASN][1000 genomes]
rs6585311	1.00[ASN][1000 genomes]
rs6585313	1.00[ASN][1000 genomes]
rs7071789	1.00[ASN][1000 genomes]
rs7071812	0.95[ASN][1000 genomes]
rs7079234	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085964	0.90[ASN][1000 genomes]
rs7086663	0.80[EUR][1000 genomes]
rs7087420	0.81[EUR][1000 genomes]
rs7090904	0.80[EUR][1000 genomes]
rs7093282	0.87[ASN][1000 genomes]
rs7093330	1.00[ASN][1000 genomes]
rs7097580	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099565	0.95[ASN][1000 genomes]
rs7099590	1.00[ASN][1000 genomes]
rs7099779	0.95[ASN][1000 genomes]
rs7100026	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100159	0.95[ASN][1000 genomes]
rs7100894	0.81[ASN][1000 genomes]
rs72836518	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769119	0.80[EUR][1000 genomes]
rs7898249	0.95[ASN][1000 genomes]
rs7904605	0.95[ASN][1000 genomes]
rs7908069	0.95[ASN][1000 genomes]
rs7908464	0.95[ASN][1000 genomes]
rs7917523	0.95[ASN][1000 genomes]
rs881192	0.95[ASN][1000 genomes]
rs968848	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968849	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv831997	chr10:116689552-116855698	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12246008	ATRNL1	cis	Muscle Skeletal	GTEx
rs12246008	TRUB1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116698800-116763600	Weak transcription	Esophagus	oesophagus
2	chr10:116742600-116763400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:116742600-116763400	Weak transcription	Lung	lung
4	chr10:116745800-116761800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:116752800-116763600	Weak transcription	Spleen	Spleen
6	chr10:116756000-116763400	Weak transcription	Fetal Brain Male	brain
7	chr10:116759200-116763400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr10:116760600-116762000	Enhancers	Brain Germinal Matrix	brain
9	chr10:116760800-116762000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr10:116760800-116762200	Enhancers	Brain Angular Gyrus	brain
11	chr10:116761000-116761800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr10:116761000-116761800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:116761000-116761800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr10:116761000-116761800	Active TSS	Ovary	ovary
15	chr10:116761000-116761800	Flanking Active TSS	HSMM	muscle
16	chr10:116761000-116761800	Flanking Active TSS	Osteobl	bone
17	chr10:116761000-116762000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:116761000-116762000	Active TSS	Stomach Smooth Muscle	stomach
19	chr10:116761000-116762400	Flanking Active TSS	GM12878-XiMat	blood
20	chr10:116761200-116761800	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr10:116761200-116761800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr10:116761200-116762400	Enhancers	Dnd41	blood
23	chr10:116761400-116761800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr10:116761400-116761800	Flanking Active TSS	HSMMtube	muscle
25	chr10:116761400-116762000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr10:116761400-116762200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr10:116761400-116762200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:116761400-116763400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:116761600-116761800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:116761600-116761800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr10:116761600-116761800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr10:116761600-116761800	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr10:116761600-116761800	Enhancers	Fetal Kidney	kidney
34	chr10:116761600-116761800	Enhancers	HepG2	liver
35	chr10:116761600-116761800	Enhancers	NHLF	lung
36	chr10:116761600-116762000	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr10:116761600-116762000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:116761600-116762000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr10:116761600-116762000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr10:116761600-116762000	Enhancers	Adipose Nuclei	Adipose
41	chr10:116761600-116762000	Enhancers	Brain Cingulate Gyrus	brain
42	chr10:116761600-116762000	Enhancers	Brain Hippocampus Middle	brain
43	chr10:116761600-116762000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr10:116761600-116762000	Enhancers	Rectal Smooth Muscle	rectum
45	chr10:116761600-116762000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr10:116761600-116762200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr10:116761600-116762200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr10:116761600-116762400	Enhancers	Aorta	Aorta
49	chr10:116761600-116763400	Weak transcription	Pancreas	Pancrea
50	chr10:116761600-116763800	Enhancers	Fetal Lung	lung

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