Variant report

Variant	rs1925175
Chromosome Location	chr6:56005788-56005789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1011277	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1016719	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1022539	0.91[LWK][hapmap];0.85[YRI][hapmap]
rs11970688	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12198041	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13193925	0.84[YRI][hapmap]
rs1474698	0.88[ASW][hapmap];0.84[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1925145	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1925152	0.84[CEU][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs1925165	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1925166	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925170	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs1925174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925185	0.95[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs1980487	0.91[LWK][hapmap];0.85[YRI][hapmap]
rs1998699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998700	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038149	0.91[LWK][hapmap];0.85[YRI][hapmap]
rs2038150	0.85[YRI][hapmap]
rs2076473	0.92[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2223598	0.81[CEU][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap]
rs2235735	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2397203	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3823468	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs3846919	0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3899394	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4119567	0.91[LWK][hapmap];0.85[YRI][hapmap]
rs4310058	0.84[JPT][hapmap];0.81[YRI][hapmap]
rs4374814	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4452633	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4607420	0.82[AFR][1000 genomes]
rs4612164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4712116	0.82[AFR][1000 genomes]
rs4712120	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs4715577	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs4715578	0.81[EUR][1000 genomes]
rs4715580	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715583	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715584	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715590	0.84[ASN][1000 genomes]
rs4715594	0.81[CEU][hapmap]
rs6459130	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6920461	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6922057	0.84[AFR][1000 genomes]
rs6926301	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6927562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6936386	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs761104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs761105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs764517	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7741903	0.81[CEU][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap]
rs7776118	0.81[CEU][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap]
rs926534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs926535	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9296827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9296831	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs9296832	0.84[CEU][hapmap];0.81[YRI][hapmap]
rs9296833	0.81[CEU][hapmap];0.81[YRI][hapmap]
rs9349804	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[YRI][hapmap]
rs9357887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9357892	0.83[AFR][1000 genomes]
rs9357893	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9367676	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9370479	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap]
rs9370482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9382584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9396172	0.81[ASN][1000 genomes]
rs9396173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9396175	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs9475556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9475558	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9475564	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9475565	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9475583	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475586	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475641	0.80[CEU][hapmap];0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1925175	FBXO9	cis	parietal	SCAN
rs1925175	ICK	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55920600-56018400	Weak transcription	Ovary	ovary
2	chr6:55967800-56008600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:55984000-56037000	Weak transcription	Fetal Kidney	kidney
4	chr6:55999000-56021200	Weak transcription	Aorta	Aorta
5	chr6:55999200-56012800	Weak transcription	Fetal Stomach	stomach
6	chr6:56002000-56007800	Weak transcription	Fetal Brain Male	brain
7	chr6:56003400-56006200	Strong transcription	Fetal Lung	lung
8	chr6:56004400-56006200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:56004600-56008200	Weak transcription	Placenta	Placenta
10	chr6:56005400-56006600	Strong transcription	Fetal Muscle Leg	muscle
11	chr6:56005400-56008400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:56005600-56006000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:56005600-56008400	Weak transcription	NHDF-Ad	bronchial

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