Variant report

Variant	rs12090485
Chromosome Location	chr1:171220626-171220627
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171219827..171222241-chr1:171222983..171225833,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206692	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10157270	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489230	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798240	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10798252	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10798253	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10912475	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10912529	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912542	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11806072	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12069067	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12078953	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12080576	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12133385	0.98[ASN][1000 genomes]
rs12405613	0.98[ASN][1000 genomes]
rs12567956	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12730305	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17350523	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1989656	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2008706	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2049922	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064078	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075987	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075990	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075991	0.94[ASN][1000 genomes]
rs2179105	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2205723	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2205727	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2205728	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2205729	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2223228	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2223232	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236874	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2421709	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421710	0.98[ASN][1000 genomes]
rs2421711	0.98[ASN][1000 genomes]
rs35152982	0.97[ASN][1000 genomes]
rs3738813	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754494	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3768570	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4480395	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916182	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916191	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916192	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425394	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425413	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6657314	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6672029	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692260	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6699803	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6701076	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703439	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7513485	0.98[ASN][1000 genomes]
rs7520777	0.96[ASN][1000 genomes]
rs7524635	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7525342	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7529080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7531713	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7531971	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7536822	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7538013	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7545923	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7553869	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7887505	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs926268	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12090485	RP1-127D3.4	cis	lung	GTEx
rs12090485	FMO2	cis	Artery Tibial	GTEx
rs12090485	RP1-127D3.4	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171217600-171221000	Active TSS	Fetal Intestine Small	intestine
2	chr1:171217600-171221200	Active TSS	Fetal Intestine Large	intestine
3	chr1:171219600-171221200	Active TSS	Fetal Lung	lung
4	chr1:171220000-171220800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:171220000-171221200	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:171220200-171220800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:171220200-171220800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:171220200-171220800	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
9	chr1:171220200-171220800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:171220200-171220800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:171220200-171220800	Active TSS	NH-A	brain
12	chr1:171220200-171221000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:171220200-171221000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:171220200-171221000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:171220200-171221000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr1:171220200-171221000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
17	chr1:171220200-171221000	Bivalent/Poised TSS	Fetal Brain Male	brain
18	chr1:171220200-171221000	Active TSS	Fetal Heart	heart
19	chr1:171220200-171221200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:171220200-171221200	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr1:171220200-171221200	Active TSS	Brain Cingulate Gyrus	brain
22	chr1:171220200-171221200	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:171220200-171221200	Active TSS	K562	blood
24	chr1:171220200-171221200	Flanking Active TSS	NHEK	skin
25	chr1:171220200-171221200	Active TSS	NHLF	lung
26	chr1:171220200-171221200	Active TSS	Osteobl	bone
27	chr1:171220200-171221400	Active TSS	Right Ventricle	heart
28	chr1:171220200-171221800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
29	chr1:171220400-171220800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:171220400-171220800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:171220400-171220800	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr1:171220400-171220800	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
33	chr1:171220400-171220800	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
34	chr1:171220400-171220800	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:171220400-171220800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:171220400-171220800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:171220400-171220800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:171220400-171220800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:171220400-171220800	Flanking Active TSS	Colonic Mucosa	Colon
40	chr1:171220400-171220800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
41	chr1:171220400-171220800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
42	chr1:171220400-171220800	Bivalent/Poised TSS	Small Intestine	intestine
43	chr1:171220400-171220800	Bivalent/Poised TSS	HSMMtube	muscle
44	chr1:171220400-171220800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
45	chr1:171220400-171221000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr1:171220400-171221000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
47	chr1:171220400-171221000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:171220400-171221000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:171220400-171221000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:171220400-171221000	Active TSS	HUES48 Cell Line	embryonic stem cell

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