Variant report

Variant	rs679249
Chromosome Location	chr6:150700095-150700096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs2064214	0.87[CHB][hapmap]
rs581697	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs588036	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606775	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs608175	0.89[CEU][hapmap]
rs609146	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs623252	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs627147	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs633945	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs634686	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs640074	0.89[CEU][hapmap]
rs641944	0.82[ASN][1000 genomes]
rs649613	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs651777	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs654116	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs654928	0.82[ASN][1000 genomes]
rs655254	0.82[ASN][1000 genomes]
rs655401	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs655745	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670292	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs671753	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs672766	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs674026	0.85[CEU][hapmap]
rs685969	0.82[ASN][1000 genomes]
rs6906028	0.85[CEU][hapmap]
rs6906229	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6930494	0.87[CHB][hapmap]
rs694326	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7757225	0.89[CEU][hapmap]
rs7771338	0.87[CHB][hapmap]
rs7772011	0.89[CEU][hapmap]
rs805989	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805991	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805992	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9322260	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs9480339	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9480340	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763602	chr6:150581193-150720666	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs679249	PPP1R14C	cis	parietal	SCAN
rs679249	RMND1	cis	cerebellum	SCAN
rs679249	ESR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150691600-150700200	Weak transcription	Lung	lung
2	chr6:150695400-150703400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:150699000-150700400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:150699000-150701600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:150699200-150701400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:150700000-150703600	Enhancers	NHDF-Ad	bronchial

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