Variant report

Variant	rs6919709
Chromosome Location	chr6:64139856-64139857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10755410	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10806206	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10806215	0.83[ASN][1000 genomes]
rs10943902	1.00[JPT][hapmap]
rs1197897	0.91[JPT][hapmap]
rs1197902	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs1197905	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs12196062	0.85[ASN][1000 genomes]
rs1322415	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1322416	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs1570315	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1620671	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1630182	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1681942	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1681946	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs1681947	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs1681957	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs1723535	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1741801	0.81[EUR][1000 genomes]
rs1744135	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs1744147	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1744152	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1779747	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1779748	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1969717	0.80[EUR][1000 genomes]
rs2076874	0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs2096346	0.81[EUR][1000 genomes]
rs2146149	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs2146150	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2186011	0.86[ASN][1000 genomes]
rs2250179	0.81[ASN][1000 genomes]
rs2622274	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2622281	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2622286	0.81[EUR][1000 genomes]
rs2622307	0.81[EUR][1000 genomes]
rs2753062	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2753066	0.81[EUR][1000 genomes]
rs2758224	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2758225	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2758237	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2758259	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs2800023	0.81[EUR][1000 genomes]
rs2800048	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2800049	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4358600	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4445042	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4543353	1.00[JPT][hapmap]
rs4710254	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4710255	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4710430	0.87[ASN][1000 genomes]
rs4710431	0.81[ASN][1000 genomes]
rs6924479	0.81[ASN][1000 genomes]
rs6929702	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6938965	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6939983	0.86[ASN][1000 genomes]
rs6942342	0.81[ASN][1000 genomes]
rs7742595	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7745873	0.87[ASN][1000 genomes]
rs7763834	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9294196	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294197	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9294198	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9294202	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9294206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294215	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9294229	0.80[ASN][1000 genomes]
rs9294234	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9294269	1.00[JPT][hapmap]
rs9341835	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9341841	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344090	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344129	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9344137	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9344168	0.86[ASN][1000 genomes]
rs9344188	0.81[ASN][1000 genomes]
rs9350929	0.81[ASN][1000 genomes]
rs9352960	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9353016	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs9359467	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9361762	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9361767	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9361779	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9361838	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9449233	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9449291	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9449297	0.87[ASN][1000 genomes]
rs9449312	0.86[ASN][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	nsv1019831	chr6:63279677-64230736	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538270	chr6:63682752-64147241	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6919709	LGSN	cis	Whole Blood	GTEx
rs6919709	SPI1	trans	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64133400-64144600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:64139800-64140200	Active TSS	Fetal Intestine Large	intestine
3	chr6:64139800-64140200	Strong transcription	A549	lung
4	chr6:64139800-64145200	Enhancers	HepG2	liver

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