Variant report

Variant	rs16834890
Chromosome Location	chr1:152999693-152999694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152999178..153000779-chr1:153005146..153007947,2	MCF-7	breast:
2	chr1:152997979..153000273-chr1:153001489..153003586,2	MCF-7	breast:
3	chr1:152997652..153000617-chr1:153004018..153006664,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169469	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10494283	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494284	1.00[AMR][1000 genomes]
rs10494286	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs10494287	1.00[AMR][1000 genomes]
rs10494289	1.00[AMR][1000 genomes]
rs1611758	0.92[MKK][hapmap];1.00[AMR][1000 genomes]
rs1611769	0.92[MKK][hapmap];1.00[AMR][1000 genomes]
rs16829001	1.00[AMR][1000 genomes]
rs16829018	0.89[ASW][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16834786	0.88[MKK][hapmap];1.00[AMR][1000 genomes]
rs16834788	0.88[MKK][hapmap];1.00[AMR][1000 genomes]
rs16834793	1.00[AMR][1000 genomes]
rs16834804	1.00[AMR][1000 genomes]
rs16834825	1.00[AMR][1000 genomes]
rs16834841	1.00[AMR][1000 genomes]
rs16834843	0.92[MKK][hapmap];1.00[AMR][1000 genomes]
rs16834855	1.00[AMR][1000 genomes]
rs16834863	0.81[ASW][hapmap];0.94[MKK][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834869	0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834878	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834888	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17878691	1.00[ASW][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17882151	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17883580	1.00[AMR][1000 genomes]
rs1933385	1.00[AMR][1000 genomes]
rs1933387	1.00[AMR][1000 genomes]
rs1998818	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28924715	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3806220	0.87[MKK][hapmap];1.00[AMR][1000 genomes]
rs3899406	1.00[ASW][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap]
rs3964618	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4378151	1.00[AMR][1000 genomes]
rs4433340	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57055311	1.00[AMR][1000 genomes]
rs57242863	1.00[AMR][1000 genomes]
rs57450008	1.00[AMR][1000 genomes]
rs57458543	1.00[AMR][1000 genomes]
rs58109785	1.00[AMR][1000 genomes]
rs58783614	1.00[AMR][1000 genomes]
rs59237147	1.00[AMR][1000 genomes]
rs59460179	1.00[AMR][1000 genomes]
rs61089580	1.00[AMR][1000 genomes]
rs73010427	1.00[AMR][1000 genomes]
rs73010429	1.00[AMR][1000 genomes]
rs73010443	1.00[AMR][1000 genomes]
rs73010447	1.00[AMR][1000 genomes]
rs73010449	1.00[AMR][1000 genomes]
rs73010452	1.00[AMR][1000 genomes]
rs73010454	1.00[AMR][1000 genomes]
rs73010458	1.00[AMR][1000 genomes]
rs73010459	1.00[AMR][1000 genomes]
rs73012481	1.00[AMR][1000 genomes]
rs73012485	1.00[AMR][1000 genomes]
rs73012496	1.00[AMR][1000 genomes]
rs73012500	1.00[AMR][1000 genomes]
rs73014324	1.00[AMR][1000 genomes]
rs73014333	1.00[AMR][1000 genomes]
rs73014337	1.00[AMR][1000 genomes]
rs73014398	1.00[AMR][1000 genomes]
rs73014402	1.00[AMR][1000 genomes]
rs73016303	1.00[AMR][1000 genomes]
rs73016322	1.00[AMR][1000 genomes]
rs883809	0.92[MKK][hapmap];1.00[AMR][1000 genomes]

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	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1003756	chr1:152944201-153044621	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv3416199	chr1:152957887-153005113	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152994200-153000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:152997200-152999800	Enhancers	NHEK	skin
3	chr1:152998600-153003000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:152999000-152999800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:152999200-153002800	Weak transcription	HMEC	breast
6	chr1:152999400-153003200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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