Variant report

Variant	rs6694387
Chromosome Location	chr1:172292205-172292206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172290966..172293542-chr1:172305681..172308662,2	MCF-7	breast:
2	chr1:172290323..172292944-chr1:172297056..172298732,2	MCF-7	breast:
3	chr1:172223489..172225833-chr1:172289738..172293302,4	MCF-7	breast:
4	chr1:172291112..172293715-chr1:172326566..172328931,2	MCF-7	breast:
5	chr1:172290799..172293766-chr1:172293837..172296183,4	MCF-7	breast:
6	chr1:172253395..172255527-chr1:172290385..172292894,2	MCF-7	breast:
7	chr1:172244510..172246522-chr1:172290374..172293118,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10158839	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs10489287	0.85[CEU][hapmap]
rs10797969	0.85[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs11590165	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12038494	0.88[EUR][1000 genomes]
rs12041600	0.88[EUR][1000 genomes]
rs12737669	0.88[EUR][1000 genomes]
rs12740971	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1992549	0.92[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1992550	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1992551	0.88[EUR][1000 genomes]
rs2224567	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs2255690	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2586393	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2586416	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2757504	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41481754	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs4916245	0.91[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6424841	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6424865	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9425287	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs9425560	0.84[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006542	chr1:172253765-172304690	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6694387	FMO1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172275200-172309800	Weak transcription	Left Ventricle	heart
2	chr1:172289600-172293200	Enhancers	Fetal Kidney	kidney
3	chr1:172289800-172292800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:172289800-172293200	Enhancers	Ovary	ovary
5	chr1:172289800-172293400	Enhancers	Fetal Muscle Leg	muscle
6	chr1:172289800-172295200	Enhancers	Fetal Stomach	stomach
7	chr1:172290000-172292400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr1:172290000-172292400	Enhancers	Brain Hippocampus Middle	brain
9	chr1:172290200-172292800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:172290200-172295600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:172290600-172292400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:172290600-172295400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:172291000-172292800	Flanking Active TSS	NHEK	skin
14	chr1:172291200-172292600	Enhancers	Fetal Brain Male	brain
15	chr1:172291200-172292600	Enhancers	Fetal Brain Female	brain
16	chr1:172291200-172292600	Flanking Active TSS	Hela-S3	cervix
17	chr1:172291200-172292800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:172291400-172292400	Active TSS	Aorta	Aorta
19	chr1:172291400-172292600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:172291400-172292600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:172291400-172292600	Enhancers	Fetal Muscle Trunk	muscle
22	chr1:172291400-172292600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr1:172291400-172292600	Flanking Active TSS	Osteobl	bone
24	chr1:172291400-172292800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:172291400-172292800	Flanking Active TSS	HMEC	breast
26	chr1:172291400-172293000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:172291400-172293000	Enhancers	Placenta	Placenta
28	chr1:172291600-172292400	Flanking Active TSS	NHLF	lung
29	chr1:172291600-172292800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:172291600-172293200	Enhancers	Brain Germinal Matrix	brain
31	chr1:172291800-172292400	Flanking Active TSS	HUVEC	blood vessel
32	chr1:172291800-172292600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:172291800-172292600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr1:172291800-172292600	Enhancers	Pancreas	Pancrea
35	chr1:172291800-172292800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:172291800-172293000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:172291800-172294800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:172292000-172292400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:172292000-172292400	Enhancers	Brain Cingulate Gyrus	brain
40	chr1:172292000-172292400	Enhancers	Fetal Lung	lung
41	chr1:172292000-172292800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr1:172292000-172293000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:172292000-172293000	Enhancers	NH-A	brain
44	chr1:172292000-172293200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:172292000-172293400	Weak transcription	Right Atrium	heart
46	chr1:172292200-172293000	Enhancers	Adipose Nuclei	Adipose
47	chr1:172292200-172293000	Enhancers	Colon Smooth Muscle	Colon
48	chr1:172292200-172293000	Enhancers	HSMM	muscle
49	chr1:172292200-172293000	Enhancers	HSMMtube	muscle
50	chr1:172292200-172293200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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