Variant report

Variant	rs353887
Chromosome Location	chr12:118650374-118650375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1092854	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1151901	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1277175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1726386	0.84[ASN][1000 genomes]
rs1726407	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs2018619	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2088702	0.88[ASW][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap]
rs2249624	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2463173	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs353885	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353889	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353890	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs353892	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353896	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs364823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs404566	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs410747	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs418941	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs456228	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs461499	0.82[ASW][hapmap];0.86[JPT][hapmap]
rs465735	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs484838	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap]
rs492939	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap]
rs494005	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs503548	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap]
rs523011	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs566437	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs571113	0.82[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap]
rs575121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs708862	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs708863	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136004	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs795473	0.94[ASN][1000 genomes]
rs795481	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs795482	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7980628	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1035497	chr12:118599539-118732144	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541612	chr12:118599539-118732144	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv524938	chr12:118624736-118740675	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs353887	GCN1L1	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118620200-118656400	Weak transcription	HepG2	liver
2	chr12:118621000-118682600	Weak transcription	A549	lung
3	chr12:118628400-118697200	Weak transcription	Psoas Muscle	Psoas
4	chr12:118628800-118672600	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:118628800-118673000	Weak transcription	NH-A	brain
6	chr12:118629800-118652400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:118636800-118658600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:118636800-118695000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:118637000-118652200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:118637200-118654400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:118637200-118700600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:118637200-118700800	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:118637400-118653600	Weak transcription	Ovary	ovary
14	chr12:118637400-118658200	Weak transcription	Brain Anterior Caudate	brain
15	chr12:118637400-118671400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:118637400-118672400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:118637400-118684200	Weak transcription	Pancreas	Pancrea
18	chr12:118637400-118694200	Weak transcription	Brain Angular Gyrus	brain
19	chr12:118637400-118701400	Weak transcription	Spleen	Spleen
20	chr12:118637400-118703800	Weak transcription	Esophagus	oesophagus
21	chr12:118637400-118724000	Weak transcription	Aorta	Aorta
22	chr12:118637600-118673000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:118638600-118651400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:118638800-118651400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:118638800-118651600	Weak transcription	Lung	lung
26	chr12:118638800-118654400	Weak transcription	Colonic Mucosa	Colon
27	chr12:118638800-118687800	Weak transcription	Gastric	stomach
28	chr12:118639000-118672200	Weak transcription	Placenta	Placenta
29	chr12:118639000-118672200	Weak transcription	Left Ventricle	heart
30	chr12:118639000-118672800	Weak transcription	Small Intestine	intestine
31	chr12:118639200-118650800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:118639200-118651400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:118639200-118651600	Weak transcription	Fetal Thymus	thymus
34	chr12:118639200-118658000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:118639200-118658200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:118639400-118651400	Weak transcription	NHEK	skin
37	chr12:118639400-118660800	Weak transcription	HSMMtube	muscle
38	chr12:118639400-118661800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:118639400-118674800	Weak transcription	HMEC	breast
40	chr12:118639800-118672600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:118643000-118672200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:118643600-118660000	Weak transcription	Fetal Stomach	stomach
43	chr12:118644200-118665600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:118644400-118651200	Weak transcription	K562	blood
45	chr12:118644800-118666400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:118645200-118655200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr12:118646000-118652200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:118646200-118652200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr12:118646800-118652200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr12:118647000-118652200	Strong transcription	Dnd41	blood

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