Variant report

Variant	rs10850754
Chromosome Location	chr12:117510936-117510937
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10744889	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10744890	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10774901	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1106277	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12423796	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1546246	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1546247	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1546248	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2173651	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4341616	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7304889	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7308236	0.85[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7959367	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7963451	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7964686	0.82[MEX][hapmap]

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	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10850754	TESC	cis	parietal	SCAN
rs10850754	BRAP	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117498800-117514600	Strong transcription	HepG2	liver
2	chr12:117499000-117522000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:117499600-117512400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:117501400-117518600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:117501600-117514800	Weak transcription	Spleen	Spleen
6	chr12:117502400-117514600	Weak transcription	Primary T cells from cord blood	blood
7	chr12:117502800-117515000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:117503000-117514600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:117503200-117515000	Weak transcription	Stomach Mucosa	stomach
10	chr12:117505400-117514800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:117505800-117514800	Weak transcription	Brain Anterior Caudate	brain
12	chr12:117508000-117515000	Weak transcription	K562	blood
13	chr12:117508200-117514200	Weak transcription	Right Atrium	heart
14	chr12:117508200-117523200	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:117508400-117512600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:117508400-117513200	Weak transcription	Left Ventricle	heart
17	chr12:117508600-117514400	Weak transcription	Fetal Thymus	thymus
18	chr12:117508600-117514600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:117508600-117520200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:117509000-117513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:117509400-117511600	Strong transcription	Gastric	stomach
22	chr12:117509400-117513400	Strong transcription	Dnd41	blood
23	chr12:117509400-117514000	Weak transcription	Fetal Heart	heart
24	chr12:117509400-117514000	Weak transcription	Pancreas	Pancrea
25	chr12:117509400-117514200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:117509800-117511600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr12:117509800-117513400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:117509800-117514400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:117509800-117514600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:117509800-117521000	Weak transcription	A549	lung
31	chr12:117510000-117513400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:117510000-117514200	Weak transcription	Right Ventricle	heart
33	chr12:117510800-117511000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:117510800-117511200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
35	chr12:117510800-117511200	Enhancers	Placenta	Placenta
36	chr12:117510800-117511200	Genic enhancers	Fetal Stomach	stomach
37	chr12:117510800-117512000	Enhancers	Fetal Muscle Leg	muscle
38	chr12:117510800-117512000	Enhancers	Ovary	ovary
39	chr12:117510800-117518600	Weak transcription	Thymus	Thymus

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