Variant report

Variant	rs16866497
Chromosome Location	chr2:179617370-179617371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10171049	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11902709	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[MEX][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12464157	1.00[AFR][1000 genomes]
rs12464703	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12470905	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12476203	1.00[AFR][1000 genomes]
rs12476289	1.00[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12477340	1.00[AFR][1000 genomes]
rs16866532	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17453396	1.00[AFR][1000 genomes]
rs17453403	1.00[AFR][1000 genomes]
rs1883084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1883085	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2243804	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs2253324	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255480	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2291304	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291305	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291308	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291309	0.87[ASN][1000 genomes]
rs2291310	0.87[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2291311	0.80[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2291312	0.80[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2306636	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2562829	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562832	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2562833	0.83[ASN][1000 genomes]
rs2562835	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2562837	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs2562841	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs2562842	0.87[ASN][1000 genomes]
rs2562852	0.93[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs2562853	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2562854	0.83[CHB][hapmap];0.87[ASN][1000 genomes]
rs2627034	0.87[ASN][1000 genomes]
rs2627037	0.93[CHB][hapmap];0.81[CHD][hapmap];0.86[ASN][1000 genomes]
rs2627040	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2627041	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2627042	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs2627044	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2742328	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2742329	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2742330	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2742332	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2742333	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs2742334	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs2742335	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs2742336	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs2742337	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2742339	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs2742340	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2742341	0.87[ASN][1000 genomes]
rs2742342	0.87[ASN][1000 genomes]
rs2742343	0.93[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs2742344	0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs2742345	0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs2742347	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742357	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3754953	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3769860	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4894037	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs55863869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55913885	1.00[AFR][1000 genomes]
rs56030306	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56120016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56142888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66677602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72647839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72647889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72648917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7585334	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7604033	0.87[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs922984	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs966783	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179483200-179655400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:179493000-179620800	Weak transcription	HSMM	muscle
3	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:179577800-179640800	Weak transcription	Fetal Intestine Large	intestine
5	chr2:179588200-179622800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr2:179590800-179640400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:179598600-179622200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:179600800-179621200	Weak transcription	Pancreas	Pancrea
9	chr2:179605400-179662400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:179610400-179621000	Strong transcription	HSMMtube	muscle
11	chr2:179610800-179671400	Weak transcription	Ovary	ovary
12	chr2:179613000-179623600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:179613400-179620000	Weak transcription	HMEC	breast
14	chr2:179614200-179626400	Strong transcription	Primary T cells from cord blood	blood
15	chr2:179614200-179645200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:179614400-179632400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:179614800-179626600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:179614800-179628800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:179615000-179618400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:179615000-179619000	Weak transcription	Left Ventricle	heart
21	chr2:179615000-179620000	Weak transcription	Right Ventricle	heart
22	chr2:179615000-179621000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:179615200-179619400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:179615400-179619000	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:179615600-179617400	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:179615800-179617400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr2:179616000-179620800	Weak transcription	Primary B cells from cord blood	blood
28	chr2:179616600-179617400	Strong transcription	Fetal Heart	heart
29	chr2:179617000-179621200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:179617200-179627800	Weak transcription	Psoas Muscle	Psoas

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