Variant report

Variant	rs1511378
Chromosome Location	chr3:140979184-140979185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11715472	0.83[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs1511376	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs1511377	0.92[EUR][1000 genomes]
rs1877219	0.94[CEU][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs1993904	0.83[GIH][hapmap]
rs2169868	0.82[CEU][hapmap]
rs2311734	0.84[EUR][1000 genomes]
rs4683398	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs4683588	0.94[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs4683592	0.83[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs6439984	0.82[CEU][hapmap]
rs6439985	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs6439990	0.88[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs6439993	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs6803258	0.83[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs6803826	0.83[CEU][hapmap]
rs899349	0.92[EUR][1000 genomes]
rs9289627	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs967526	0.90[GIH][hapmap]
rs9841326	0.82[CEU][hapmap]
rs9878866	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1511378	TAC3	trans	parietal	SCAN
rs1511378	OR2A12	trans	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140955200-140980600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:140960000-140980000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:140961200-140985800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
8	chr3:140961400-140983200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:140962000-140985800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:140962400-140979200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:140962600-140979600	Weak transcription	Fetal Intestine Large	intestine
12	chr3:140962600-140980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:140963400-140982800	Weak transcription	Brain Germinal Matrix	brain
14	chr3:140966000-140990200	Weak transcription	Psoas Muscle	Psoas
15	chr3:140966200-140979600	Weak transcription	Pancreas	Pancrea
16	chr3:140968200-140990000	Weak transcription	Gastric	stomach
17	chr3:140968400-140982800	Weak transcription	Fetal Lung	lung
18	chr3:140974800-140985800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:140974800-140987400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:140974800-140991400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:140975000-140979200	Weak transcription	Brain Angular Gyrus	brain
22	chr3:140975000-140979400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:140975000-140979400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:140975000-140979800	Weak transcription	Brain Substantia Nigra	brain
25	chr3:140975000-140984800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:140975000-140985800	Weak transcription	Right Atrium	heart
27	chr3:140975000-140993400	Weak transcription	Lung	lung
28	chr3:140975000-140993400	Weak transcription	Spleen	Spleen
29	chr3:140975200-140980600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:140975200-140984400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:140975200-140984800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:140975200-140985000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:140975200-140991800	Weak transcription	Placenta	Placenta
34	chr3:140975400-140979400	Weak transcription	Left Ventricle	heart
35	chr3:140975400-140979600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:140975400-140980000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:140975400-140980600	Weak transcription	HSMM	muscle
38	chr3:140975400-140983400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:140975400-140990200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:140975800-140979200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:140975800-140979800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:140975800-140980000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:140975800-140983600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:140975800-140993200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:140976000-140983600	Weak transcription	Fetal Brain Female	brain
46	chr3:140976400-140987200	Weak transcription	Fetal Brain Male	brain
47	chr3:140976600-140985800	Weak transcription	Fetal Heart	heart
48	chr3:140977000-140980000	Genic enhancers	Thymus	Thymus
49	chr3:140977200-140980000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:140977200-140985200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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