Variant report

Variant	rs1412540
Chromosome Location	chr6:131326392-131326393
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1006655	0.81[CEU][hapmap]
rs1977578	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1984054	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2327005	0.93[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4897479	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6902768	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6932317	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7746714	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761655	0.81[CEU][hapmap]
rs9375786	0.81[CEU][hapmap]
rs9388877	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9388881	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9402304	0.81[CEU][hapmap]
rs9402305	0.87[CEU][hapmap]
rs9402307	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9402312	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs946348	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9483203	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9483204	0.83[LWK][hapmap];0.82[YRI][hapmap]
rs9492789	0.82[YRI][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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1412540	TAAR1	cis	cerebellum	SCAN
rs1412540	C6orf192	cis	cerebellum	SCAN
rs1412540	AKAP7	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131318800-131328000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:131318800-131329200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:131321000-131326600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr6:131321800-131327200	Enhancers	Fetal Stomach	stomach
5	chr6:131322400-131327000	Enhancers	Brain Substantia Nigra	brain
6	chr6:131322600-131326600	Enhancers	Brain Hippocampus Middle	brain
7	chr6:131322600-131326800	Enhancers	Brain Cingulate Gyrus	brain
8	chr6:131322600-131327000	Enhancers	Brain Anterior Caudate	brain
9	chr6:131322600-131327000	Enhancers	Fetal Lung	lung
10	chr6:131322600-131333200	Weak transcription	Pancreas	Pancrea
11	chr6:131323600-131326600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:131323600-131327000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr6:131323600-131327800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:131323600-131328200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:131323800-131327000	Enhancers	NHLF	lung
16	chr6:131323800-131328000	Weak transcription	A549	lung
17	chr6:131323800-131328200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:131324000-131334200	Weak transcription	Small Intestine	intestine
19	chr6:131324200-131326800	Enhancers	Fetal Heart	heart
20	chr6:131324400-131326800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:131324600-131326400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:131324600-131327200	Enhancers	Fetal Muscle Leg	muscle
23	chr6:131324600-131327400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:131324800-131328000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:131325000-131326600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:131325000-131326600	Enhancers	Left Ventricle	heart
27	chr6:131325000-131327000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr6:131325000-131327000	Enhancers	Ovary	ovary
29	chr6:131325000-131327000	Enhancers	K562	blood
30	chr6:131325200-131327200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:131325200-131328000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:131325400-131327800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:131325600-131326400	Enhancers	Stomach Mucosa	stomach
34	chr6:131325600-131326600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:131325600-131326600	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr6:131325600-131327000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:131325800-131326800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:131325800-131326800	Enhancers	Placenta	Placenta
39	chr6:131325800-131327000	Enhancers	NHDF-Ad	bronchial
40	chr6:131326000-131326800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:131326000-131327000	Weak transcription	Right Atrium	heart
42	chr6:131326000-131328000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:131326000-131328000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:131326000-131329400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:131326000-131333800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:131326200-131326800	Enhancers	Adipose Nuclei	Adipose
47	chr6:131326200-131328000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:131326200-131328400	Weak transcription	Fetal Muscle Trunk	muscle

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