Variant report

Variant	rs12869081
Chromosome Location	chr13:76100090-76100091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1050235	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11148993	0.87[CEU][hapmap]
rs12146901	0.84[AMR][1000 genomes]
rs12146907	0.84[AMR][1000 genomes]
rs12859594	0.80[EUR][1000 genomes]
rs12859711	0.80[EUR][1000 genomes]
rs12861744	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs12861774	0.82[EUR][1000 genomes]
rs12865529	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12866747	0.80[EUR][1000 genomes]
rs12871445	0.82[EUR][1000 genomes]
rs17064647	0.94[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2031234	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs34072684	0.80[EUR][1000 genomes]
rs34241221	0.80[EUR][1000 genomes]
rs34407556	0.80[EUR][1000 genomes]
rs34572351	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34949196	0.80[EUR][1000 genomes]
rs35132045	0.80[EUR][1000 genomes]
rs35132275	0.82[EUR][1000 genomes]
rs35352582	0.80[EUR][1000 genomes]
rs35556048	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35596538	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35631959	0.82[EUR][1000 genomes]
rs35680815	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35853105	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35901810	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36043532	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885298	0.87[CEU][hapmap]
rs4885299	0.87[GIH][hapmap];0.85[MEX][hapmap]
rs4885302	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885303	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885304	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885310	0.85[EUR][1000 genomes]
rs4885311	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs4885315	0.80[EUR][1000 genomes]
rs4885327	0.80[EUR][1000 genomes]
rs6562904	1.00[EUR][1000 genomes]
rs6562905	0.83[CEU][hapmap]
rs6562910	0.80[EUR][1000 genomes]
rs66528354	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66635712	0.80[EUR][1000 genomes]
rs66808557	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67051742	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67211435	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67270540	0.80[EUR][1000 genomes]
rs67532736	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67656352	0.80[EUR][1000 genomes]
rs68017902	0.80[EUR][1000 genomes]
rs68044755	0.82[EUR][1000 genomes]
rs68052366	0.80[EUR][1000 genomes]
rs71215998	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7321611	0.80[EUR][1000 genomes]
rs7324560	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7325969	0.83[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs7337186	0.82[CEU][hapmap]
rs9530443	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9530444	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9543938	0.81[CEU][hapmap]
rs9543943	0.87[CEU][hapmap]
rs9543950	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9543952	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9543953	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9543961	0.89[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9543962	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9573581	0.83[CEU][hapmap]
rs9593081	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv900562	chr13:76072743-76176680	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900563	chr13:76093935-76169347	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv900564	chr13:76100090-76156136	Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12869081	UCHL3	cis	parietal	SCAN
rs12869081	ENSG00000188243	cis	multi-tissue	Pritchard
rs12869081	LMO7	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76089000-76104800	Weak transcription	NHDF-Ad	bronchial
2	chr13:76093600-76109400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:76094400-76101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr13:76095600-76109200	Weak transcription	Gastric	stomach
5	chr13:76095800-76111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:76096600-76101800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr13:76096600-76107400	Weak transcription	Fetal Intestine Small	intestine
8	chr13:76096600-76110400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:76096600-76111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:76096800-76104400	Weak transcription	Primary B cells from cord blood	blood
11	chr13:76097000-76111000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:76097000-76111600	Weak transcription	Spleen	Spleen
13	chr13:76097400-76104800	Weak transcription	GM12878-XiMat	blood
14	chr13:76097400-76106200	Weak transcription	Brain Hippocampus Middle	brain
15	chr13:76097600-76106200	Weak transcription	Fetal Lung	lung
16	chr13:76097600-76107400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:76097800-76101000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr13:76097800-76107200	Weak transcription	Fetal Stomach	stomach
19	chr13:76097800-76110400	Weak transcription	Brain Angular Gyrus	brain
20	chr13:76097800-76110600	Weak transcription	Fetal Brain Male	brain
21	chr13:76097800-76110600	Weak transcription	Fetal Kidney	kidney
22	chr13:76097800-76110600	Weak transcription	Psoas Muscle	Psoas
23	chr13:76097800-76111200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr13:76098000-76100600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr13:76098000-76101000	Weak transcription	NH-A	brain
26	chr13:76098000-76104200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr13:76098000-76107600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr13:76098000-76110400	Weak transcription	A549	lung
29	chr13:76098000-76110400	Weak transcription	HUVEC	blood vessel
30	chr13:76098000-76110600	Weak transcription	Brain Anterior Caudate	brain
31	chr13:76098000-76110600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr13:76098000-76111200	Weak transcription	Aorta	Aorta
33	chr13:76098200-76107400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr13:76098200-76107400	Weak transcription	NHLF	lung
35	chr13:76098200-76108200	Weak transcription	NHEK	skin
36	chr13:76098200-76109600	Weak transcription	Brain Germinal Matrix	brain
37	chr13:76098200-76110400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr13:76098400-76103800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr13:76098400-76110200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr13:76098600-76104400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr13:76098600-76111000	Weak transcription	Colonic Mucosa	Colon
42	chr13:76098800-76110400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr13:76098800-76111400	Weak transcription	Esophagus	oesophagus
44	chr13:76099200-76101400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:76099200-76102400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr13:76099200-76104200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr13:76099200-76107400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr13:76099400-76100200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr13:76099400-76100200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr13:76099400-76100200	Strong transcription	Adipose Nuclei	Adipose

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