Variant report

Variant	rs12092388
Chromosome Location	chr1:76240652-76240653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1001160	1.00[JPT][hapmap]
rs10873797	1.00[JPT][hapmap]
rs11161465	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs11161598	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161688	0.81[EUR][1000 genomes]
rs11161718	0.80[EUR][1000 genomes]
rs11161848	1.00[JPT][hapmap]
rs11161902	1.00[JPT][hapmap]
rs11163917	0.80[EUR][1000 genomes]
rs11163928	0.80[EUR][1000 genomes]
rs11163967	1.00[JPT][hapmap]
rs1144340	0.81[EUR][1000 genomes]
rs1146598	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146607	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146609	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146610	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146617	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146630	0.86[ASN][1000 genomes]
rs1146631	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1146632	0.80[EUR][1000 genomes]
rs1146634	0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs1146635	0.89[GIH][hapmap]
rs1146636	0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs1146637	0.80[EUR][1000 genomes]
rs1146644	0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs11578480	1.00[JPT][hapmap]
rs11588643	1.00[JPT][hapmap]
rs1159215	1.00[JPT][hapmap]
rs12022011	0.88[CEU][hapmap]
rs12043473	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs12044025	0.81[CEU][hapmap]
rs12045299	0.86[CEU][hapmap]
rs12130832	1.00[JPT][hapmap]
rs12131344	1.00[JPT][hapmap]
rs12132750	1.00[JPT][hapmap]
rs12142247	1.00[JPT][hapmap]
rs12732722	0.86[CEU][hapmap]
rs12734931	0.81[EUR][1000 genomes]
rs12744608	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs1323735	0.81[EUR][1000 genomes]
rs1332786	0.80[EUR][1000 genomes]
rs1463812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498311	1.00[JPT][hapmap]
rs1628063	1.00[JPT][hapmap]
rs1630587	1.00[JPT][hapmap]
rs1689270	1.00[JPT][hapmap]
rs17647178	1.00[JPT][hapmap]
rs1770889	1.00[JPT][hapmap]
rs1796813	1.00[JPT][hapmap]
rs1796815	1.00[JPT][hapmap]
rs1796827	1.00[JPT][hapmap]
rs1856791	1.00[JPT][hapmap]
rs2029682	1.00[JPT][hapmap]
rs211713	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs211719	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs4638068	1.00[JPT][hapmap]
rs5745323	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs5745325	1.00[JPT][hapmap]
rs5745331	1.00[JPT][hapmap]
rs5745347	1.00[JPT][hapmap]
rs5745383	1.00[JPT][hapmap]
rs5745394	1.00[JPT][hapmap]
rs5745430	1.00[JPT][hapmap]
rs5745543	1.00[JPT][hapmap]
rs5745545	1.00[JPT][hapmap]
rs5745547	1.00[JPT][hapmap]
rs6593520	0.89[GIH][hapmap];1.00[JPT][hapmap]
rs6593521	1.00[JPT][hapmap]
rs6656501	1.00[JPT][hapmap]
rs6695055	0.86[CEU][hapmap]
rs721204	1.00[JPT][hapmap]
rs7533542	0.80[EUR][1000 genomes]
rs7548991	0.86[CEU][hapmap];0.82[TSI][hapmap]
rs7552289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814853	0.80[EUR][1000 genomes]
rs814875	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap]
rs814876	0.95[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs9660848	0.86[CEU][hapmap];0.82[TSI][hapmap]

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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	esv2763563	chr1:76229839-76245374	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12092388	AK5	cis	parietal	SCAN
rs12092388	RABGGTB	cis	parietal	SCAN
rs12092388	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs12092388	ACADM	cis	cerebellum	SCAN
rs12092388	MSH4	cis	parietal	SCAN
rs12092388	MSH4	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76227400-76249800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:76232800-76243200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:76234000-76241000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:76234600-76241200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:76238000-76241200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:76238200-76241000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:76238200-76241400	Weak transcription	NHEK	skin
8	chr1:76240600-76241400	Enhancers	K562	blood

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