Variant report

Variant	rs1040228
Chromosome Location	chr2:181980885-181980886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10176421	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10184839	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10184846	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10191559	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10194653	0.95[ASN][1000 genomes]
rs10204666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207887	0.98[ASN][1000 genomes]
rs10208742	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1040229	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1046193	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10930952	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1107786	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs11902472	0.98[ASN][1000 genomes]
rs11902868	1.00[ASN][1000 genomes]
rs12151685	0.91[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12468438	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1356549	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1401124	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs1401125	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs1401126	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs1401128	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1401131	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1401133	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1401134	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1401135	0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1518451	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1518452	0.82[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap]
rs1518455	0.91[CHB][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1518456	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs1518460	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1568258	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17668214	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs2048976	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs2048977	0.91[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap]
rs2090558	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2139060	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2139061	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2176550	0.82[ASN][1000 genomes]
rs2368189	0.91[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2368190	0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2368191	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2368194	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3792220	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4077213	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs4077924	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563182	0.84[JPT][hapmap]
rs4575685	0.83[EUR][1000 genomes]
rs4666662	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4666663	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4666668	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs4666669	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs4666684	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4666685	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4666991	0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap]
rs4666996	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4666997	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs4667004	0.91[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs4667020	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs4667030	0.80[EUR][1000 genomes]
rs4667035	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4667041	0.91[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4667082	1.00[ASN][1000 genomes]
rs55639120	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55851371	0.82[EUR][1000 genomes]
rs56206103	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56970984	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57230918	0.82[EUR][1000 genomes]
rs58057770	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60513343	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61483341	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62178778	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62178779	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62178780	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62178781	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62178784	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62178785	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62180157	0.80[EUR][1000 genomes]
rs62181564	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181565	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181569	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181570	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181571	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181572	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181573	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62181575	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62181577	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62181579	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62181580	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433880	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs6433881	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6433885	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6433887	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433891	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433893	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704963	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs6709398	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6716258	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6725837	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6731523	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs6737752	0.86[ASN][1000 genomes]
rs6747525	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs6747797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6754913	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6759130	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72885232	0.80[EUR][1000 genomes]
rs72885247	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72885292	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72887003	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7349233	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7370006	0.91[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7370048	0.91[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7371242	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7371259	0.91[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7565130	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575113	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs7578218	0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs908734	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs908736	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431824	chr2:181946115-182118559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv459954	chr2:181975252-182040293	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv583910	chr2:181975252-182040293	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1040228	LOC729026	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:181973800-181985000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr2:181974000-181985200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:181980200-181981400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:181980800-181981000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr2:181980800-181981400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:181980800-181982800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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