Variant report

Variant	rs561417
Chromosome Location	chr22:27604149-27604150
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:27602742..27604550-chr22:27607695..27610449,2	MCF-7	breast:
2	chr22:27592803..27595348-chr22:27602254..27604254,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs491735	0.89[ASN][1000 genomes]
rs492416	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs494604	0.89[ASN][1000 genomes]
rs497365	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs497368	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs499712	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs499733	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs500281	0.87[ASN][1000 genomes]
rs555860	0.91[ASN][1000 genomes]
rs849449	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs864754	0.87[ASN][1000 genomes]
rs9613395	0.85[CEU][hapmap]
rs9613399	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917333	chr22:26931825-27692024	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	142 gene(s)	inside rSNPs	diseases
2	esv34168	chr22:27289097-27678031	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs561417	VPREB1	cis	cerebellum	SCAN
rs561417	SEZ6L	cis	cerebellum	SCAN
rs561417	CCDC116	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27593600-27608800	Weak transcription	Right Atrium	heart
2	chr22:27598400-27607800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr22:27599600-27608600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr22:27599800-27606200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:27600800-27604600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr22:27601400-27604800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr22:27601600-27604200	Enhancers	Fetal Muscle Leg	muscle
8	chr22:27601600-27604600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr22:27601800-27604400	Enhancers	NHEK	skin
10	chr22:27601800-27604600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr22:27601800-27604600	Enhancers	NH-A	brain
12	chr22:27602000-27606200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr22:27602000-27606200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr22:27602000-27606200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr22:27602200-27604600	Enhancers	A549	lung
16	chr22:27602200-27604800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr22:27602400-27608200	Weak transcription	HSMM	muscle
18	chr22:27602800-27604600	Enhancers	Esophagus	oesophagus
19	chr22:27602800-27605800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr22:27603000-27609600	Weak transcription	Aorta	Aorta
21	chr22:27603400-27604600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr22:27603600-27604200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:27603600-27604400	Enhancers	Adipose Nuclei	Adipose
24	chr22:27603600-27604600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr22:27603600-27604600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr22:27603600-27604800	Enhancers	Osteobl	bone
27	chr22:27603800-27604200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr22:27603800-27604200	Bivalent Enhancer	NHDF-Ad	bronchial
29	chr22:27603800-27604200	Enhancers	NHLF	lung
30	chr22:27603800-27604400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr22:27603800-27604600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr22:27603800-27604600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr22:27603800-27604600	Active TSS	Spleen	Spleen

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