Variant report

Variant	rs16824540
Chromosome Location	chr3:154790081-154790082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:154788960..154792081-chr3:154794108..154796605,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10513467	0.83[AMR][1000 genomes]
rs16824527	0.83[AMR][1000 genomes]
rs16824533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16824536	1.00[CEU][hapmap]
rs17442246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1836912	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];1.00[EUR][1000 genomes]
rs34851137	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34860880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4414805	0.83[AMR][1000 genomes]
rs55862533	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56317942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56380855	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56393356	1.00[EUR][1000 genomes]
rs57022891	0.83[AMR][1000 genomes]
rs58120007	0.83[AMR][1000 genomes]
rs60351120	0.83[AMR][1000 genomes]
rs60435073	0.83[AMR][1000 genomes]
rs60948062	0.83[AMR][1000 genomes]
rs6805925	0.97[AFR][1000 genomes]
rs73874449	1.00[AMR][1000 genomes]
rs73874454	0.83[AMR][1000 genomes]
rs73874476	0.83[AMR][1000 genomes]
rs73874478	0.83[AMR][1000 genomes]
rs73874489	0.83[AMR][1000 genomes]
rs7643334	0.83[AMR][1000 genomes]
rs9917802	0.83[AMR][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	nsv868930	chr3:154076125-154820242	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1000140	chr3:154336261-154905740	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv534289	chr3:154535584-154987166	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv532663	chr3:154561578-154960353	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:154785200-154790600	Enhancers	NHDF-Ad	bronchial
2	chr3:154786600-154790200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:154786800-154790200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:154787600-154790200	Enhancers	NHLF	lung
5	chr3:154789000-154796600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:154789200-154794200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:154789200-154796200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:154789200-154796400	Weak transcription	HMEC	breast
9	chr3:154789200-154797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:154789400-154796400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:154789600-154796200	Weak transcription	Osteobl	bone
12	chr3:154789600-154796400	Weak transcription	HUVEC	blood vessel
13	chr3:154789600-154796600	Weak transcription	HSMMtube	muscle

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