Variant report

Variant	rs41481754
Chromosome Location	chr1:172294597-172294598
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172294512..172295506-chr1:172329394..172330284,2	MCF-7	breast:
2	chr1:172290799..172293766-chr1:172293837..172296183,4	MCF-7	breast:
3	chr1:172293750..172296257-chr1:172325539..172327779,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10158839	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797965	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10797969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1992549	0.84[CEU][hapmap]
rs2224567	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586393	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs2586416	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs4916245	0.90[CEU][hapmap]
rs6424865	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs6694387	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs9425286	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425287	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425288	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425559	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963874	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41481754	FMO1	cis	parietal	SCAN
rs41481754	SFT2D2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172275200-172309800	Weak transcription	Left Ventricle	heart
2	chr1:172289800-172295200	Enhancers	Fetal Stomach	stomach
3	chr1:172290200-172295600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:172290600-172295400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:172291800-172294800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:172292600-172297400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:172292800-172294600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:172292800-172294800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:172292800-172303600	Weak transcription	Aorta	Aorta
10	chr1:172293000-172294600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:172293000-172294600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:172293000-172295200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:172293000-172297400	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:172293200-172294600	Weak transcription	Osteobl	bone
15	chr1:172293200-172294800	Weak transcription	Fetal Kidney	kidney
16	chr1:172293200-172294800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:172293200-172294800	Weak transcription	NHLF	lung
18	chr1:172293800-172295000	Enhancers	Fetal Muscle Leg	muscle
19	chr1:172293800-172295600	Enhancers	HMEC	breast
20	chr1:172293800-172295600	Enhancers	NHEK	skin
21	chr1:172294000-172295000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:172294000-172295400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:172294000-172295400	Enhancers	Fetal Lung	lung
24	chr1:172294200-172295200	Enhancers	Fetal Intestine Small	intestine
25	chr1:172294200-172295400	Flanking Active TSS	A549	lung
26	chr1:172294200-172295400	Enhancers	NH-A	brain
27	chr1:172294200-172295600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:172294200-172295600	Enhancers	Colon Smooth Muscle	Colon
29	chr1:172294200-172295600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr1:172294200-172295800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:172294400-172294600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:172294400-172294600	Enhancers	Fetal Muscle Trunk	muscle
33	chr1:172294400-172295000	Enhancers	Rectal Smooth Muscle	rectum
34	chr1:172294400-172295400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:172294400-172295600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:172294400-172295600	Enhancers	Hela-S3	cervix
37	chr1:172294400-172295600	Enhancers	HUVEC	blood vessel
38	chr1:172294400-172295600	Enhancers	NHDF-Ad	bronchial
39	chr1:172294400-172295800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:172294400-172295800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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