Variant report

Variant	rs200962
Chromosome Location	chr6:27875697-27875698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs149854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs149879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs149898	0.85[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs156741	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs156742	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16867901	1.00[EUR][1000 genomes]
rs169263	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs175953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs175955	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1770132	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs183926	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200959	0.84[YRI][hapmap]
rs200970	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs203867	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs203874	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2200870	1.00[EUR][1000 genomes]
rs2622318	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276364	1.00[YRI][hapmap]
rs276366	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276367	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276368	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276372	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs366113	1.00[AMR][1000 genomes]
rs425159	0.85[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55965630	1.00[EUR][1000 genomes]
rs56221999	1.00[EUR][1000 genomes]
rs56262840	1.00[EUR][1000 genomes]
rs56366090	1.00[EUR][1000 genomes]
rs58700542	1.00[EUR][1000 genomes]
rs60554811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73739606	1.00[EUR][1000 genomes]
rs73739685	1.00[EUR][1000 genomes]
rs73740805	1.00[EUR][1000 genomes]
rs73740842	1.00[EUR][1000 genomes]
rs839777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9295739	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
3	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
4	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
5	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs200962	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27871600-27883200	Weak transcription	Hela-S3	cervix
2	chr6:27872200-27876200	Strong transcription	K562	blood
3	chr6:27875600-27876200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27875600-27876200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:27875600-27876200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:27875600-27876200	Enhancers	HMEC	breast
7	chr6:27875600-27876400	Enhancers	NHEK	skin

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