Variant report

Variant	rs16828827
Chromosome Location	chr2:188164094-188164095
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:188163565..188166308-chr2:188168308..188169936,2	K562	blood:
2	chr2:188163616..188164504-chr2:188317553..188318396,2	MCF-7	breast:
3	chr2:188163672..188164442-chr2:188307237..188307741,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs16828851	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16828854	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16828891	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16828917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16828925	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16829012	0.81[CHB][hapmap]
rs1706259	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2268300	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs3771063	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs3771082	0.81[ASN][1000 genomes]
rs3771085	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41393945	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs4667161	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55637608	0.83[ASN][1000 genomes]
rs55785596	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55887912	0.83[ASN][1000 genomes]
rs55907979	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56035809	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56045439	0.81[ASN][1000 genomes]
rs56235386	0.83[ASN][1000 genomes]
rs57732150	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59832815	0.83[ASN][1000 genomes]
rs61080294	0.80[EUR][1000 genomes]
rs61343122	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73979866	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73979869	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73981136	0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73981186	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73981187	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73981194	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73981195	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8176447	1.00[YRI][hapmap]
rs8176513	1.00[YRI][hapmap]
rs8176614	1.00[CEU][hapmap]
rs840565	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs840579	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840598	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs840599	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9288141	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949700	chr2:187713412-188361211	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1003061	chr2:187950057-188282330	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1000617	chr2:187950057-188290511	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533935	chr2:188089148-188284766	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188162400-188166800	Enhancers	HUVEC	blood vessel
2	chr2:188162600-188164200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:188162800-188164200	Weak transcription	Adipose Nuclei	Adipose
4	chr2:188163000-188164200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:188163000-188167000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:188163200-188167000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:188163200-188167000	Weak transcription	HSMM	muscle
8	chr2:188164000-188164200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:188164000-188164600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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