Variant report

Variant	rs6667928
Chromosome Location	chr1:154114705-154114706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154108211..154110544-chr1:154113165..154115090,2	K562	blood:
2	chr1:154112503..154115575-chr1:154116263..154118766,3	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1051370	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10559	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs10908558	0.95[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs10908627	0.91[ASW][hapmap]
rs10908723	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264680	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs11264743	0.95[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs11264866	0.91[ASW][hapmap]
rs11264871	0.90[YRI][hapmap]
rs11264873	0.82[YRI][hapmap]
rs11264875	0.83[ASW][hapmap];0.82[YRI][hapmap]
rs11264886	0.82[YRI][hapmap]
rs11264964	0.83[ASW][hapmap];1.00[YRI][hapmap]
rs11264974	0.82[YRI][hapmap]
rs11265049	1.00[YRI][hapmap]
rs11265076	1.00[YRI][hapmap]
rs11265082	0.91[ASW][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs11265099	0.95[LWK][hapmap];0.83[MKK][hapmap]
rs11265122	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265299	0.86[JPT][hapmap]
rs12021641	0.91[ASW][hapmap];0.87[LWK][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap]
rs12026475	0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs12048137	0.82[YRI][hapmap]
rs1212352	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs12405309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12408170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408458	0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap]
rs12564669	0.88[YRI][hapmap]
rs3196889	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3791187	0.82[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs3828076	0.86[JPT][hapmap]
rs4521985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs4845600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55677228	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6664278	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs6671166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6672856	0.83[ASW][hapmap]
rs6673171	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6678826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs6680140	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs6693620	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6701341	0.91[ASW][hapmap]
rs72696227	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517127	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7521303	1.00[YRI][hapmap]
rs7535778	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7547663	1.00[YRI][hapmap]
rs7552737	0.91[ASW][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap]
rs8450	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs946682	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv872451	chr1:154101519-154139757	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6667928	SLC39A1	cis	cerebellum	SCAN
rs6667928	FLG	cis	parietal	SCAN
rs6667928	SPRR2D	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154112200-154138400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154114000-154115200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:154114600-154126800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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