Variant report

Variant	rs2246353
Chromosome Location	chr12:106809177-106809178
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10778483	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10778484	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10861600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861607	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10861615	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11112983	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113012	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11113015	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11113016	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11113020	0.80[AMR][1000 genomes]
rs12231768	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13561	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1532586	1.00[LWK][hapmap]
rs1882413	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2243506	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245062	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249773	0.94[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250262	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250441	1.00[LWK][hapmap]
rs2250653	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2252685	0.85[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2253054	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2253838	0.80[GIH][hapmap]
rs2254755	0.85[CHB][hapmap]
rs2288266	0.82[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2288269	0.85[AMR][1000 genomes]
rs2374609	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34619628	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851635	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3902141	0.80[AMR][1000 genomes]
rs4964460	0.80[GIH][hapmap];0.82[MEX][hapmap]
rs6539261	1.00[LWK][hapmap]
rs6539262	1.00[LWK][hapmap]
rs7137444	0.80[CHB][hapmap]
rs7137638	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs741624	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2246353	POLR3B	Cis_1M	lymphoblastoid	RTeQTL
rs2246353	TCP11L2	cis	cerebellum	SCAN
rs2246353	NUAK1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106753000-106811800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:106753000-106815400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:106764000-106821000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:106764400-106811800	Weak transcription	HUVEC	blood vessel
5	chr12:106773000-106828000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:106774400-106834000	Weak transcription	Small Intestine	intestine
7	chr12:106774600-106819000	Weak transcription	Right Ventricle	heart
8	chr12:106774800-106811800	Weak transcription	NHEK	skin
9	chr12:106776800-106821800	Weak transcription	Brain Angular Gyrus	brain
10	chr12:106779600-106821800	Weak transcription	Brain Substantia Nigra	brain
11	chr12:106782000-106810000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:106783600-106818800	Weak transcription	Fetal Heart	heart
13	chr12:106787000-106830200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:106787600-106856600	Weak transcription	GM12878-XiMat	blood
15	chr12:106787800-106852400	Weak transcription	Gastric	stomach
16	chr12:106787800-106852800	Weak transcription	Pancreas	Pancrea
17	chr12:106788000-106827200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:106789000-106829800	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:106789200-106811800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:106789200-106821400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:106789400-106812400	Weak transcription	Brain Anterior Caudate	brain
22	chr12:106789400-106819000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:106789400-106821800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:106789600-106810400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:106790000-106819000	Weak transcription	Lung	lung
26	chr12:106790200-106811800	Weak transcription	HepG2	liver
27	chr12:106790400-106811800	Weak transcription	Adipose Nuclei	Adipose
28	chr12:106790400-106821000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:106791800-106811800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:106791800-106817200	Weak transcription	Aorta	Aorta
31	chr12:106791800-106819000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:106791800-106821200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:106792000-106810000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:106792000-106810000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:106792000-106810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:106792000-106811800	Weak transcription	Ovary	ovary
37	chr12:106792000-106817200	Weak transcription	Esophagus	oesophagus
38	chr12:106792000-106819000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:106792000-106821400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr12:106792000-106827800	Weak transcription	Fetal Intestine Large	intestine
41	chr12:106792200-106810200	Weak transcription	Fetal Intestine Small	intestine
42	chr12:106800000-106828200	Weak transcription	K562	blood
43	chr12:106800200-106815800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:106800400-106810200	Weak transcription	Fetal Stomach	stomach
45	chr12:106800600-106811800	Weak transcription	Fetal Lung	lung
46	chr12:106802400-106854000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:106802800-106810600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:106803200-106811800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:106803200-106828400	Weak transcription	Fetal Thymus	thymus
50	chr12:106803600-106811200	Strong transcription	Primary monocytes fromperipheralblood	blood

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