Variant report

Variant	rs2486995
Chromosome Location	chr1:179098475-179098476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179097406..179100383-chr1:179127242..179129431,2	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1078872	0.89[EUR][1000 genomes]
rs10913690	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913692	0.89[ASN][1000 genomes]
rs10913695	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913696	0.85[ASN][1000 genomes]
rs10913697	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1173077	0.88[EUR][1000 genomes]
rs12130276	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1325195	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1856967	0.98[EUR][1000 genomes]
rs1856968	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858551	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066279	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2087559	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2130576	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2171959	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2258217	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2258221	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486997	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2486998	0.92[ASN][1000 genomes]
rs2493123	0.86[ASN][1000 genomes]
rs2493124	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636265	0.89[EUR][1000 genomes]
rs2636274	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636275	0.82[ASN][1000 genomes]
rs2636276	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636277	0.82[ASN][1000 genomes]
rs2636280	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636281	0.89[EUR][1000 genomes]
rs2636282	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2636287	0.98[EUR][1000 genomes]
rs2636291	0.91[ASN][1000 genomes]
rs2791936	0.90[ASN][1000 genomes]
rs2791940	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2791941	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2791942	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2791943	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2791944	0.87[ASN][1000 genomes]
rs2791945	0.85[ASN][1000 genomes]
rs2793790	0.90[ASN][1000 genomes]
rs2793793	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793794	0.92[ASN][1000 genomes]
rs2793795	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793796	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793797	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793798	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793799	0.89[EUR][1000 genomes]
rs2793803	0.91[EUR][1000 genomes]
rs2793806	0.88[EUR][1000 genomes]
rs2793812	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816166	0.93[ASN][1000 genomes]
rs2816167	0.89[EUR][1000 genomes]
rs2816183	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816184	0.90[ASN][1000 genomes]
rs2816185	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816186	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2816187	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816189	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2816191	0.87[ASN][1000 genomes]
rs2816196	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816197	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816198	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816199	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816202	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816203	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816204	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816206	0.91[EUR][1000 genomes]
rs2816208	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2816209	0.91[EUR][1000 genomes]
rs2816210	0.87[EUR][1000 genomes]
rs2816211	0.91[EUR][1000 genomes]
rs2816214	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3210839	0.95[EUR][1000 genomes]
rs36122838	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377785	0.89[EUR][1000 genomes]
rs3813642	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3813643	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3829794	0.89[ASN][1000 genomes]
rs411266	0.89[EUR][1000 genomes]
rs434283	0.89[EUR][1000 genomes]
rs451088	0.89[EUR][1000 genomes]
rs4651012	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4651013	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652357	0.82[EUR][1000 genomes]
rs7555921	0.86[ASN][1000 genomes]
rs7556011	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs915337	0.89[EUR][1000 genomes]
rs9286921	0.92[ASN][1000 genomes]
rs965401	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9662858	0.89[ASN][1000 genomes]
rs9726961	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727252	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9728480	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729129	0.92[ASN][1000 genomes]
rs9729199	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012667	chr1:179094571-179120280	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002253	chr1:179094571-179120938	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1001191	chr1:179097246-179120938	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2486995	TOR3A	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179063200-179112000	Weak transcription	Fetal Kidney	kidney
2	chr1:179079600-179109800	Weak transcription	Small Intestine	intestine
3	chr1:179080000-179098600	Weak transcription	Esophagus	oesophagus
4	chr1:179080200-179101600	Weak transcription	Fetal Brain Male	brain
5	chr1:179080400-179103800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:179080800-179099000	Weak transcription	Colonic Mucosa	Colon
7	chr1:179080800-179099000	Weak transcription	Spleen	Spleen
8	chr1:179086600-179105000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:179086800-179099000	Weak transcription	Right Ventricle	heart
10	chr1:179087800-179113000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:179088000-179098600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:179088000-179099000	Weak transcription	Aorta	Aorta
13	chr1:179088200-179098800	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:179088200-179102400	Weak transcription	Brain Germinal Matrix	brain
15	chr1:179088400-179099200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:179088400-179099400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:179088600-179098800	Weak transcription	Ovary	ovary
18	chr1:179088600-179098800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:179089200-179099400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:179089600-179099000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:179090800-179099200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:179090800-179104400	Weak transcription	Fetal Brain Female	brain
23	chr1:179091000-179098600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:179091000-179098800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:179091000-179098800	Weak transcription	Brain Angular Gyrus	brain
26	chr1:179091000-179098800	Weak transcription	Thymus	Thymus
27	chr1:179091000-179108800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:179091000-179109000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:179091000-179109200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:179093400-179117200	Weak transcription	Fetal Stomach	stomach
31	chr1:179093600-179099000	Genic enhancers	Muscle Satellite Cultured Cells	--
32	chr1:179093800-179098800	Genic enhancers	HSMM	muscle
33	chr1:179093800-179098800	Genic enhancers	NHDF-Ad	bronchial
34	chr1:179093800-179099000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:179093800-179099600	Genic enhancers	HMEC	breast
36	chr1:179094000-179099600	Genic enhancers	Osteobl	bone
37	chr1:179094400-179099600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:179094600-179098800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:179095200-179099800	Genic enhancers	NHEK	skin
40	chr1:179095400-179098600	Enhancers	Liver	Liver
41	chr1:179095600-179101000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:179095800-179098600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:179095800-179098600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:179095800-179098800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:179095800-179098800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:179095800-179098800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:179095800-179098800	Weak transcription	Psoas Muscle	Psoas
48	chr1:179095800-179099000	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:179095800-179099400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:179095800-179100800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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