Variant report

Variant	rs2083066
Chromosome Location	chr15:60095464-60095465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1036514	0.86[ASN][1000 genomes]
rs10468018	0.95[ASN][1000 genomes]
rs10851665	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11071479	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11071480	0.95[ASN][1000 genomes]
rs11071488	0.87[ASN][1000 genomes]
rs11071489	0.89[ASN][1000 genomes]
rs11630357	0.91[ASN][1000 genomes]
rs11632455	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11633326	0.91[ASN][1000 genomes]
rs11633484	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11635283	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636295	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593427	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12594880	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595753	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12898608	0.87[ASN][1000 genomes]
rs12915893	0.94[ASN][1000 genomes]
rs1437475	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1437476	0.91[ASN][1000 genomes]
rs1437477	0.91[ASN][1000 genomes]
rs1437478	0.91[ASN][1000 genomes]
rs1437479	0.91[ASN][1000 genomes]
rs1437482	0.88[ASN][1000 genomes]
rs1437487	0.92[CEU][hapmap]
rs1561249	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16941757	0.83[ASN][1000 genomes]
rs16953426	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17302727	0.96[ASN][1000 genomes]
rs1866052	0.92[ASN][1000 genomes]
rs1866053	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1866056	0.81[ASN][1000 genomes]
rs1866057	0.81[ASN][1000 genomes]
rs1898447	0.83[ASN][1000 genomes]
rs2008741	1.00[CEU][hapmap]
rs2083065	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196607	0.91[ASN][1000 genomes]
rs2414647	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2414648	0.91[ASN][1000 genomes]
rs28499099	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28665953	0.88[ASN][1000 genomes]
rs2917824	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2917826	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2917827	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2960787	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2960788	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2960800	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2960813	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2960814	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2965329	0.91[ASN][1000 genomes]
rs2965331	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2965333	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2965334	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2965335	0.80[ASN][1000 genomes]
rs2970366	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2970367	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2970368	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2970374	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2970375	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34835177	0.88[ASN][1000 genomes]
rs35380618	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4080182	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4620904	0.87[MEX][hapmap]
rs4774343	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4774344	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775205	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs4775210	0.88[ASN][1000 genomes]
rs4775211	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4775212	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4775213	0.81[ASN][1000 genomes]
rs4995778	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs55752605	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55887443	0.94[ASN][1000 genomes]
rs60653843	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6494146	0.91[ASN][1000 genomes]
rs6494147	0.97[ASN][1000 genomes]
rs6494148	0.81[ASN][1000 genomes]
rs7162699	0.84[ASN][1000 genomes]
rs7163595	0.84[ASN][1000 genomes]
rs7163623	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs7165175	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166798	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7167046	0.84[ASN][1000 genomes]
rs7169841	0.91[ASN][1000 genomes]
rs7173468	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173653	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174331	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7174483	0.80[ASN][1000 genomes]
rs7176324	0.89[ASN][1000 genomes]
rs7177418	0.88[ASN][1000 genomes]
rs7179349	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7181522	0.91[ASN][1000 genomes]
rs7182438	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7182646	0.83[ASN][1000 genomes]
rs7182978	0.91[ASN][1000 genomes]
rs7183185	0.91[ASN][1000 genomes]
rs8027629	0.94[ASN][1000 genomes]
rs8030694	0.83[ASN][1000 genomes]
rs8031153	0.84[ASN][1000 genomes]
rs8032951	1.00[MEX][hapmap]
rs965353	0.87[CEU][hapmap];0.81[CHB][hapmap];0.93[MEX][hapmap]
rs965355	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs9972499	0.84[ASN][1000 genomes]
rs9972503	0.85[ASN][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	nsv904280	chr15:60042722-60524025	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2083066	MNS1	cis	parietal	SCAN
rs2083066	TREML1	trans	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:60085000-60095600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:60089200-60095600	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr15:60089800-60097000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr15:60091000-60095600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr15:60091000-60095600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr15:60092000-60095600	Enhancers	Primary T cells fromperipheralblood	blood
7	chr15:60092600-60095600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:60093400-60095800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr15:60095000-60095600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr15:60095200-60095600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:60095200-60095600	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr15:60095200-60095600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:60095200-60096200	Enhancers	Thymus	Thymus
14	chr15:60095200-60096200	Active TSS	A549	lung
15	chr15:60095200-60096400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:60095400-60095600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr15:60095400-60095600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:60095400-60095600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:60095400-60095600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr15:60095400-60095600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr15:60095400-60095600	Enhancers	Dnd41	blood
22	chr15:60095400-60095800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr15:60095400-60095800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr15:60095400-60095800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr15:60095400-60095800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:60095400-60095800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr15:60095400-60096000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr15:60095400-60096000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr15:60095400-60096000	Enhancers	HepG2	liver
30	chr15:60095400-60096000	Enhancers	NHEK	skin
31	chr15:60095400-60096200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr15:60095400-60096400	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr15:60095400-60096400	Enhancers	Fetal Thymus	thymus

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