Variant report

Variant	rs2816213
Chromosome Location	chr1:179183766-179183767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1078872	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913690	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10913692	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs10913695	0.91[EUR][1000 genomes]
rs10913697	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs1173077	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs12130276	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs1325194	0.88[GIH][hapmap]
rs1325195	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1763022	0.88[ASN][1000 genomes]
rs1807916	0.88[ASN][1000 genomes]
rs1826183	0.88[ASN][1000 genomes]
rs1856967	0.89[EUR][1000 genomes]
rs1856968	0.92[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1858551	0.91[EUR][1000 genomes]
rs2050923	0.89[ASN][1000 genomes]
rs2066279	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2087559	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2130576	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2171958	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2171959	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs2258217	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2258221	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2306941	0.86[ASN][1000 genomes]
rs2486995	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2486997	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2487563	0.89[ASN][1000 genomes]
rs2493124	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs2636265	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636266	0.88[GIH][hapmap];0.80[TSI][hapmap]
rs2636272	0.89[ASN][1000 genomes]
rs2636274	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2636276	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2636277	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs2636280	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636281	0.99[EUR][1000 genomes]
rs2636282	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636287	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs2636290	0.93[GIH][hapmap]
rs2636293	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2791940	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2791941	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2791942	0.81[EUR][1000 genomes]
rs2791943	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2791944	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2793790	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2793793	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2793795	0.85[EUR][1000 genomes]
rs2793796	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs2793797	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs2793798	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2793799	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs2793801	0.88[ASN][1000 genomes]
rs2793802	0.90[ASN][1000 genomes]
rs2793803	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793805	0.88[GIH][hapmap]
rs2793806	0.95[EUR][1000 genomes]
rs2793810	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2793812	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793813	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2793816	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2816166	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816167	0.99[EUR][1000 genomes]
rs2816168	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2816183	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2816184	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816185	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2816186	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2816187	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2816189	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2816190	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816191	0.81[ASN][1000 genomes]
rs2816193	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2816196	0.91[EUR][1000 genomes]
rs2816197	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816198	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816199	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816200	0.85[ASN][1000 genomes]
rs2816201	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816202	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816203	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816204	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816206	0.98[EUR][1000 genomes]
rs2816207	0.91[ASN][1000 genomes]
rs2816208	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816209	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs2816210	0.96[EUR][1000 genomes]
rs2816211	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816212	0.86[ASN][1000 genomes]
rs2816214	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816218	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs3121198	0.84[ASN][1000 genomes]
rs3122376	0.86[ASN][1000 genomes]
rs3210839	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs36122838	0.88[EUR][1000 genomes]
rs377785	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813642	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs3813643	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs3818433	0.93[GIH][hapmap]
rs3829794	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs411266	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs413613	0.87[ASN][1000 genomes]
rs434283	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs451088	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4651012	0.88[EUR][1000 genomes]
rs4651013	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6668200	0.84[YRI][hapmap]
rs915337	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425839	0.91[ASN][1000 genomes]
rs965401	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9662858	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9726961	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9727252	0.91[EUR][1000 genomes]
rs9728480	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs9729199	0.88[EUR][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	esv3417804	chr1:179183648-179183804	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2816213	TOR3A	cis	Artery Tibial	GTEx
rs2816213	IER5	cis	cerebellum	SCAN
rs2816213	FAM20B	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179117800-179186000	Weak transcription	Fetal Stomach	stomach
2	chr1:179122000-179189400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:179139400-179196800	Weak transcription	Pancreas	Pancrea
4	chr1:179148000-179186000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:179148400-179185800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:179157400-179197400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:179157400-179197600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:179160200-179186800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:179160800-179188000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:179169000-179197400	Weak transcription	NHEK	skin
11	chr1:179170200-179184000	Weak transcription	Fetal Intestine Small	intestine
12	chr1:179170200-179197200	Weak transcription	Fetal Intestine Large	intestine
13	chr1:179171800-179186600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:179172200-179186600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:179172800-179189800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:179173000-179187600	Weak transcription	Small Intestine	intestine
17	chr1:179174800-179184000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr1:179174800-179186600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:179175200-179189200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:179176200-179185000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:179176200-179186800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:179176200-179187000	Weak transcription	NHDF-Ad	bronchial
23	chr1:179176200-179187200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:179176200-179195800	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:179176200-179195800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:179176200-179196600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:179176200-179197600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:179176400-179187800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:179176400-179196200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:179176400-179197000	Weak transcription	Fetal Brain Male	brain
31	chr1:179176400-179197400	Weak transcription	Fetal Lung	lung
32	chr1:179176400-179197600	Weak transcription	Left Ventricle	heart
33	chr1:179176600-179196200	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:179176800-179189400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:179177000-179196000	Weak transcription	Fetal Brain Female	brain
36	chr1:179177000-179197600	Weak transcription	HSMMtube	muscle
37	chr1:179177400-179197200	Weak transcription	Brain Germinal Matrix	brain
38	chr1:179177800-179196600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:179178000-179196000	Weak transcription	Aorta	Aorta
40	chr1:179178000-179197600	Weak transcription	Gastric	stomach
41	chr1:179178400-179185800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:179178400-179189400	Weak transcription	HepG2	liver
43	chr1:179178400-179189600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:179178400-179197600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:179178600-179186200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:179178600-179187000	Weak transcription	Liver	Liver
47	chr1:179178600-179187000	Weak transcription	HUVEC	blood vessel
48	chr1:179178600-179189000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:179178600-179197600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:179178600-179197600	Weak transcription	NH-A	brain

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