Variant report

Variant	rs7967117
Chromosome Location	chr12:4876033-4876034
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10047570	0.91[ASN][1000 genomes]
rs10160902	0.82[ASN][1000 genomes]
rs10431361	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10431362	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849125	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10849126	0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs10849127	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10849128	0.80[ASN][1000 genomes]
rs10849129	0.91[ASN][1000 genomes]
rs10849130	0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10849131	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10849133	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10849137	0.95[ASN][1000 genomes]
rs10849138	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849139	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10849143	1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs11063314	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11063318	0.91[ASN][1000 genomes]
rs11063327	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11063328	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11063331	0.98[ASN][1000 genomes]
rs12296205	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12320374	0.95[ASN][1000 genomes]
rs1468556	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs17783373	0.82[ASN][1000 genomes]
rs2018895	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2109099	0.82[ASN][1000 genomes]
rs2109100	0.82[ASN][1000 genomes]
rs2159354	0.83[ASN][1000 genomes]
rs2159355	0.83[ASN][1000 genomes]
rs2191157	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2286578	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2286580	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2286581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2359466	0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2359467	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs35049745	0.82[ASN][1000 genomes]
rs3782740	0.81[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs3782741	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3782742	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3782743	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4765779	0.82[ASN][1000 genomes]
rs4765781	0.81[ASN][1000 genomes]
rs4765782	0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4765784	0.94[EUR][1000 genomes]
rs4766272	0.81[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs4766276	0.82[ASN][1000 genomes]
rs4766278	0.82[ASN][1000 genomes]
rs4766279	0.82[ASN][1000 genomes]
rs4766280	0.82[ASN][1000 genomes]
rs4766281	0.82[ASN][1000 genomes]
rs4766282	0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4766283	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs4766286	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6489558	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6489560	0.81[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs6489565	0.95[ASN][1000 genomes]
rs6489566	0.95[ASN][1000 genomes]
rs6489567	0.94[ASN][1000 genomes]
rs7132030	0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7137040	0.82[ASN][1000 genomes]
rs7137660	0.82[ASN][1000 genomes]
rs7295230	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7295251	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7297290	0.91[ASN][1000 genomes]
rs7305387	0.95[ASN][1000 genomes]
rs7305525	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7306235	0.82[ASN][1000 genomes]
rs7311475	0.82[ASN][1000 genomes]
rs7311675	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7311694	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7312119	0.82[ASN][1000 genomes]
rs7314849	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315211	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7316209	0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs766504	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs766505	0.96[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7953170	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs7953399	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7953482	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7966628	0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs7970126	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7972019	0.82[ASN][1000 genomes]
rs7973527	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7975978	0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7976011	0.95[ASN][1000 genomes]
rs7976219	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs929481	0.99[ASN][1000 genomes]
rs9300304	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][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	nsv1054218	chr12:4819576-4882667	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3332578	chr12:4874835-4877804	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7967117	SLC2A14	cis	parietal	SCAN
rs7967117	LOC653113	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4867200-4880200	Weak transcription	Spleen	Spleen
2	chr12:4869800-4884200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:4871800-4877800	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:4873000-4876400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:4873200-4879800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:4873200-4881800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:4873200-4889800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:4873400-4876200	Weak transcription	Right Atrium	heart
9	chr12:4873400-4876600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:4873400-4881200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:4873400-4889400	Weak transcription	Ovary	ovary
12	chr12:4873600-4876200	Weak transcription	Brain Germinal Matrix	brain
13	chr12:4874600-4881000	Weak transcription	Fetal Brain Female	brain
14	chr12:4875000-4876200	Weak transcription	Right Ventricle	heart
15	chr12:4875000-4878200	Enhancers	Fetal Muscle Leg	muscle
16	chr12:4875600-4876400	Enhancers	Adipose Nuclei	Adipose
17	chr12:4875600-4876800	Enhancers	Left Ventricle	heart
18	chr12:4875600-4877800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:4875600-4879400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:4875600-4881400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:4876000-4876600	Enhancers	Fetal Brain Male	brain
22	chr12:4876000-4876600	Enhancers	Fetal Stomach	stomach
23	chr12:4876000-4877600	Weak transcription	Fetal Lung	lung

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