Variant report

Variant	rs10489297
Chromosome Location	chr1:172149515-172149516
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172146908..172150355-chr1:172151675..172155662,5	MCF-7	breast:
2	chr1:172147006..172149581-chr1:172326946..172329408,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10910941	1.00[CHB][hapmap]
rs10911270	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11484597	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584955	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589142	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123837	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126381	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129806	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135520	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843855	1.00[CHB][hapmap]
rs16843860	1.00[CHB][hapmap]
rs17277008	1.00[CHB][hapmap]
rs17277127	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277372	0.91[GIH][hapmap];0.90[TSI][hapmap]
rs17346438	1.00[CHB][hapmap]
rs17346452	1.00[CHB][hapmap]
rs17346473	1.00[CHB][hapmap]
rs17350544	1.00[CHB][hapmap]
rs17350579	1.00[CHB][hapmap]
rs17350586	1.00[CHB][hapmap]
rs17361789	1.00[CHB][hapmap]
rs17361886	1.00[ASW][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361955	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2209096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209098	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224782	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421990	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421991	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915514	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394690	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540689	1.00[CHB][hapmap]
rs479960	0.80[MEX][hapmap]
rs55935473	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138708	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583578	0.80[MEX][hapmap]
rs593688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807788	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694089	1.00[CHB][hapmap]
rs7535241	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979021	0.99[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	nsv1000079	chr1:172146935-172230545	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489297	FMO1	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172128400-172149800	Weak transcription	Aorta	Aorta
2	chr1:172132800-172150000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:172138400-172149800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:172142200-172149600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:172145800-172150000	Weak transcription	Psoas Muscle	Psoas
6	chr1:172146400-172149600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:172146600-172150200	Enhancers	Stomach Mucosa	stomach
8	chr1:172146800-172152000	Enhancers	Fetal Intestine Small	intestine
9	chr1:172147400-172154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:172147600-172149600	Enhancers	Small Intestine	intestine
11	chr1:172147600-172151200	Enhancers	Fetal Intestine Large	intestine
12	chr1:172148000-172149800	Enhancers	Colon Smooth Muscle	Colon
13	chr1:172148200-172149600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:172148200-172149800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:172148200-172149800	Enhancers	Duodenum Mucosa	Duodenum
16	chr1:172148800-172149800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:172148800-172149800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:172148800-172152000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr1:172149000-172149600	Enhancers	Primary B cells from cord blood	blood
20	chr1:172149000-172149600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr1:172149000-172149800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:172149000-172149800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:172149000-172149800	Enhancers	Fetal Kidney	kidney
24	chr1:172149000-172149800	Enhancers	Fetal Muscle Leg	muscle
25	chr1:172149000-172149800	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:172149000-172149800	Enhancers	NHDF-Ad	bronchial
27	chr1:172149000-172150000	Enhancers	Primary T cells from cord blood	blood
28	chr1:172149000-172150000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:172149000-172150000	Enhancers	Brain Angular Gyrus	brain
30	chr1:172149000-172150000	Enhancers	Brain Cingulate Gyrus	brain
31	chr1:172149000-172150000	Enhancers	Brain Substantia Nigra	brain
32	chr1:172149000-172150400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:172149000-172152800	Enhancers	Fetal Stomach	stomach
34	chr1:172149200-172150000	Enhancers	Primary B cells from peripheral blood	blood
35	chr1:172149200-172150000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:172149200-172150000	Enhancers	Brain Anterior Caudate	brain
37	chr1:172149200-172150200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:172149200-172150600	Enhancers	Brain Hippocampus Middle	brain
39	chr1:172149400-172149600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:172149400-172149600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr1:172149400-172149600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:172149400-172149800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:172149400-172149800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:172149400-172149800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr1:172149400-172149800	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr1:172149400-172150000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr1:172149400-172150000	Enhancers	Fetal Lung	lung
48	chr1:172149400-172150000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr1:172149400-172150000	Flanking Active TSS	GM12878-XiMat	blood
50	chr1:172149400-172150000	Enhancers	HSMM	muscle

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