Variant report

Variant	rs2816209
Chromosome Location	chr1:179171494-179171495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1046385	0.85[JPT][hapmap]
rs1078872	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs10798652	0.95[JPT][hapmap];0.83[MEX][hapmap]
rs10913690	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10913695	0.91[EUR][1000 genomes]
rs10913697	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1173077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12130276	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1325194	0.93[GIH][hapmap];0.81[JPT][hapmap]
rs1325195	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs17362081	0.80[JPT][hapmap]
rs1856967	0.91[EUR][1000 genomes]
rs1856968	0.92[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1858551	0.91[EUR][1000 genomes]
rs2066279	1.00[CEU][hapmap];0.83[JPT][hapmap];0.99[EUR][1000 genomes]
rs2087559	0.94[EUR][1000 genomes]
rs2130576	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs2171959	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2258217	0.92[EUR][1000 genomes]
rs2258221	0.89[EUR][1000 genomes]
rs2486995	0.91[EUR][1000 genomes]
rs2486997	0.91[EUR][1000 genomes]
rs2493124	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2636265	0.97[EUR][1000 genomes]
rs2636266	0.92[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs2636274	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2636276	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2636280	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs2636281	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636282	0.98[EUR][1000 genomes]
rs2636287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2636289	0.81[AMR][1000 genomes]
rs2636290	0.97[GIH][hapmap];0.81[JPT][hapmap]
rs2791940	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs2791941	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2791942	0.81[EUR][1000 genomes]
rs2791943	0.92[EUR][1000 genomes]
rs2793793	0.94[EUR][1000 genomes]
rs2793795	0.85[EUR][1000 genomes]
rs2793796	0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2793797	0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2793798	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs2793799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793803	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs2793804	0.81[AMR][1000 genomes]
rs2793805	0.92[GIH][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs2793806	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793807	0.81[AMR][1000 genomes]
rs2793812	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs2793816	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap]
rs2816167	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816183	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs2816185	0.91[EUR][1000 genomes]
rs2816186	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2816187	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs2816189	0.93[EUR][1000 genomes]
rs2816196	0.91[EUR][1000 genomes]
rs2816197	0.94[EUR][1000 genomes]
rs2816198	0.96[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs2816199	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs2816201	0.82[JPT][hapmap]
rs2816202	0.95[EUR][1000 genomes]
rs2816203	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs2816204	0.95[EUR][1000 genomes]
rs2816206	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816208	0.99[EUR][1000 genomes]
rs2816210	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2816211	0.98[EUR][1000 genomes]
rs2816213	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap]
rs2816214	1.00[CEU][hapmap];0.82[JPT][hapmap];0.99[EUR][1000 genomes]
rs3210839	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs36122838	0.88[EUR][1000 genomes]
rs377785	0.97[EUR][1000 genomes]
rs3813642	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs3813643	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs3818433	0.97[GIH][hapmap];0.80[TSI][hapmap]
rs411266	1.00[CEU][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes]
rs434283	0.97[EUR][1000 genomes]
rs451088	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs4651012	0.88[EUR][1000 genomes]
rs4651013	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs4651014	0.81[JPT][hapmap]
rs61821690	0.81[AMR][1000 genomes]
rs6681864	0.89[YRI][hapmap]
rs915337	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs931441	0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs9650996	1.00[YRI][hapmap]
rs9650997	0.95[YRI][hapmap]
rs965401	0.93[EUR][1000 genomes]
rs9726961	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs9727252	0.91[EUR][1000 genomes]
rs9728480	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs9729199	0.88[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2816209	FAM20B	cis	lymphoblastoid	seeQTL
rs2816209	FAM20B	cis	parietal	SCAN
rs2816209	IER5	cis	cerebellum	SCAN
rs2816209	TOR3A	cis	Artery Tibial	GTEx

Chromatin state (count:38 , 50 per page) page: 1

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	chr1:179146800-179175600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:179147600-179174600	Weak transcription	Psoas Muscle	Psoas
6	chr1:179148000-179186000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:179148400-179185800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:179150600-179176000	Weak transcription	HSMM	muscle
9	chr1:179150800-179178000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:179150800-179180400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:179154000-179171600	Weak transcription	Primary T cells from cord blood	blood
12	chr1:179156400-179177800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:179157400-179197400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:179157400-179197600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:179157600-179177800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:179159400-179176000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:179160200-179186800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:179160400-179171600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:179160400-179174600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:179160800-179188000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:179162800-179177800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:179163800-179172000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:179167800-179177800	Weak transcription	Fetal Heart	heart
24	chr1:179169000-179197400	Weak transcription	NHEK	skin
25	chr1:179169400-179174600	Weak transcription	Fetal Brain Female	brain
26	chr1:179169600-179181200	Weak transcription	GM12878-XiMat	blood
27	chr1:179170200-179172400	Weak transcription	Small Intestine	intestine
28	chr1:179170200-179175200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:179170200-179184000	Weak transcription	Fetal Intestine Small	intestine
30	chr1:179170200-179197200	Weak transcription	Fetal Intestine Large	intestine
31	chr1:179170400-179174400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:179170800-179175600	Weak transcription	Brain Substantia Nigra	brain
33	chr1:179171000-179171800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:179171200-179172000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:179171200-179174400	Weak transcription	Ovary	ovary
36	chr1:179171400-179171800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:179171400-179172000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr1:179171400-179172600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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