Variant report

Variant	rs6424865
Chromosome Location	chr1:172290932-172290933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172290323..172292944-chr1:172297056..172298732,2	MCF-7	breast:
2	chr1:172223489..172225833-chr1:172289738..172293302,4	MCF-7	breast:
3	chr1:172290799..172293766-chr1:172293837..172296183,4	MCF-7	breast:
4	chr1:172063383..172065738-chr1:172289085..172291783,2	MCF-7	breast:
5	chr1:172290820..172291829-chr1:172368303..172369352,3	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: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10158839	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs10489287	0.80[CEU][hapmap]
rs10797969	0.80[CEU][hapmap];0.86[TSI][hapmap]
rs11590165	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12038494	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12041600	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12737669	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12740971	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1992549	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1992550	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1992551	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2224567	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs2255690	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586393	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586416	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2757504	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41481754	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs4916245	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508742	0.88[ASW][hapmap]
rs6424841	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6694387	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]
rs9425283	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9425287	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs9425560	0.80[CEU][hapmap];0.88[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
rs6424865	FMO1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172272600-172291600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:172275200-172309800	Weak transcription	Left Ventricle	heart
3	chr1:172289600-172293200	Enhancers	Fetal Kidney	kidney
4	chr1:172289800-172291000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:172289800-172291200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:172289800-172291200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:172289800-172291200	Enhancers	Adipose Nuclei	Adipose
8	chr1:172289800-172291200	Flanking Active TSS	A549	lung
9	chr1:172289800-172291200	Enhancers	Hela-S3	cervix
10	chr1:172289800-172291400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:172289800-172291400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:172289800-172291400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:172289800-172291400	Enhancers	Colon Smooth Muscle	Colon
14	chr1:172289800-172291400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:172289800-172291400	Enhancers	HSMM	muscle
16	chr1:172289800-172291600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:172289800-172291800	Enhancers	Fetal Lung	lung
18	chr1:172289800-172291800	Enhancers	Rectal Smooth Muscle	rectum
19	chr1:172289800-172292800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:172289800-172293200	Enhancers	Ovary	ovary
21	chr1:172289800-172293400	Enhancers	Fetal Muscle Leg	muscle
22	chr1:172289800-172295200	Enhancers	Fetal Stomach	stomach
23	chr1:172290000-172291000	Enhancers	NHEK	skin
24	chr1:172290000-172291800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:172290000-172292400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr1:172290000-172292400	Enhancers	Brain Hippocampus Middle	brain
27	chr1:172290200-172291000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:172290200-172291000	Flanking Active TSS	Osteobl	bone
29	chr1:172290200-172291400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:172290200-172291400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:172290200-172291400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:172290200-172291400	Enhancers	HMEC	breast
33	chr1:172290200-172291600	Enhancers	NHLF	lung
34	chr1:172290200-172292200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr1:172290200-172292800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:172290200-172295600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:172290400-172292200	Flanking Active TSS	HSMMtube	muscle
38	chr1:172290400-172292200	Flanking Active TSS	NHDF-Ad	bronchial
39	chr1:172290600-172291000	Enhancers	HUVEC	blood vessel
40	chr1:172290600-172291200	Weak transcription	Fetal Brain Female	brain
41	chr1:172290600-172291400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:172290600-172291400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:172290600-172291400	Enhancers	Stomach Smooth Muscle	stomach
44	chr1:172290600-172291600	Enhancers	NH-A	brain
45	chr1:172290600-172291800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:172290600-172291800	Enhancers	Stomach Mucosa	stomach
47	chr1:172290600-172292200	Enhancers	Brain Substantia Nigra	brain
48	chr1:172290600-172292400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:172290600-172295400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:172290800-172291000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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