Variant report

Variant	rs2816187
Chromosome Location	chr1:179101606-179101607
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1078872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10913690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913692	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10913695	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913696	0.85[ASN][1000 genomes]
rs10913697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1173077	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs12130276	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1325195	0.89[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1856967	0.97[EUR][1000 genomes]
rs1856968	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858551	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2087559	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2130576	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2171958	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2171959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2258217	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2258221	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486995	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486997	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2486998	0.92[ASN][1000 genomes]
rs2493123	0.86[ASN][1000 genomes]
rs2493124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636265	0.90[EUR][1000 genomes]
rs2636274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636277	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2636280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636281	0.90[EUR][1000 genomes]
rs2636282	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2636287	0.96[CEU][hapmap];0.81[JPT][hapmap];0.98[EUR][1000 genomes]
rs2636291	0.91[ASN][1000 genomes]
rs2636293	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2791936	0.90[ASN][1000 genomes]
rs2791940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2791941	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2791942	0.84[AMR][1000 genomes];0.89[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	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2791945	0.85[ASN][1000 genomes]
rs2793790	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2793793	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793794	0.92[ASN][1000 genomes]
rs2793795	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793796	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793797	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793799	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs2793803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs2793806	0.88[EUR][1000 genomes]
rs2793810	1.00[CHB][hapmap]
rs2793812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2793813	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2793816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2816166	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2816167	0.90[EUR][1000 genomes]
rs2816168	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816184	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2816185	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2816189	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2816190	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816191	0.87[ASN][1000 genomes]
rs2816193	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816196	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816197	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816201	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs2816202	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];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	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs2816210	0.87[EUR][1000 genomes]
rs2816211	0.91[EUR][1000 genomes]
rs2816213	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs2816214	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2816218	0.96[CHB][hapmap]
rs3210839	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes]
rs36122838	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377785	0.90[EUR][1000 genomes]
rs3813642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3813643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3829794	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs411266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs434283	0.90[EUR][1000 genomes]
rs451088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4651012	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4651013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652357	0.81[EUR][1000 genomes]
rs6668200	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs7555921	0.86[ASN][1000 genomes]
rs7556011	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs915337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs9286921	0.92[ASN][1000 genomes]
rs965401	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9662858	0.96[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs9726961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727252	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9728480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729129	0.92[ASN][1000 genomes]
rs9729199	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[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
rs2816187	TOR3A	cis	Artery Tibial	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

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	chr1:179080400-179103800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:179086600-179105000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:179087800-179113000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:179088200-179102400	Weak transcription	Brain Germinal Matrix	brain
7	chr1:179090800-179104400	Weak transcription	Fetal Brain Female	brain
8	chr1:179091000-179108800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:179091000-179109000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:179091000-179109200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:179093400-179117200	Weak transcription	Fetal Stomach	stomach
12	chr1:179095800-179101800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:179095800-179103600	Weak transcription	Fetal Intestine Large	intestine
14	chr1:179095800-179106800	Weak transcription	Gastric	stomach
15	chr1:179095800-179107400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:179096400-179108800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:179096600-179106800	Weak transcription	Fetal Lung	lung
18	chr1:179096600-179110200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:179098200-179112000	Weak transcription	Lung	lung
20	chr1:179099200-179110200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:179099200-179110400	Weak transcription	Brain Angular Gyrus	brain
22	chr1:179099200-179110400	Weak transcription	Brain Anterior Caudate	brain
23	chr1:179099200-179114800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:179099400-179103400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:179099400-179106800	Weak transcription	Pancreas	Pancrea
26	chr1:179099400-179106800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:179099400-179106800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:179099400-179107000	Weak transcription	Placenta	Placenta
29	chr1:179099400-179110000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:179099400-179110400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:179099400-179112000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:179099400-179112000	Weak transcription	Left Ventricle	heart
33	chr1:179099600-179103400	Strong transcription	NH-A	brain
34	chr1:179099600-179103800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:179099600-179106800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:179099600-179106800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:179099600-179109200	Weak transcription	Primary T cells from cord blood	blood
38	chr1:179099600-179109800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:179099600-179109800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:179099600-179110000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:179099600-179110200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:179099600-179110600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:179099600-179110800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:179099600-179116800	Weak transcription	Thymus	Thymus
45	chr1:179099600-179119400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:179099600-179122600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:179099800-179102000	Weak transcription	GM12878-XiMat	blood
48	chr1:179099800-179104000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:179099800-179106400	Weak transcription	Hela-S3	cervix
50	chr1:179099800-179107000	Weak transcription	Adipose Nuclei	Adipose

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