Variant report

Variant	rs2205581
Chromosome Location	chr21:16990673-16990674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:16985973..16987583-chr21:16990550..16993331,2	MCF-7	breast:
2	chr21:16989283..16990838-chr21:17003947..17006454,2	MCF-7	breast:
3	chr21:16990382..16992239-chr21:17100657..17103328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212564	Chromatin interaction
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1041405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150374	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205579	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242854	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2823383	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2823385	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2823387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823389	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2823392	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823393	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4309648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127894	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8129126	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8129450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130341	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8130709	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133897	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8134573	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9305675	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9981405	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064280	chr21:16664312-17049272	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv2758530	chr21:16912646-17096678	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2758810	chr21:16912646-17096678	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1062105	chr21:16956885-17141961	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv544380	chr21:16956885-17141961	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv2830057	chr21:16960590-17113148	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2205581	USP25	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16989000-16991200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr21:16989200-16991200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr21:16989200-16991200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr21:16989200-16991200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr21:16989400-16991200	Enhancers	HSMM	muscle
6	chr21:16989600-16990800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:16989600-16990800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr21:16989800-16991000	Enhancers	Hela-S3	cervix
9	chr21:16989800-16991000	Enhancers	HMEC	breast
10	chr21:16989800-16991400	Enhancers	HSMMtube	muscle
11	chr21:16990000-16991000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr21:16990000-16991000	Enhancers	NH-A	brain
13	chr21:16990000-16991200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr21:16990000-16991200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr21:16990000-16991200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr21:16990200-16990800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr21:16990200-16990800	Enhancers	HUVEC	blood vessel
18	chr21:16990400-16990800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:16990400-16990800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr21:16990400-16990800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr21:16990400-16990800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr21:16990400-16990800	Flanking Active TSS	A549	lung
23	chr21:16990400-16990800	Enhancers	NHEK	skin
24	chr21:16990400-16991000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr21:16990400-16991000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr21:16990400-16991000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr21:16990400-16991400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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