Variant report

Variant	rs454902
Chromosome Location	chr21:40486933-40486934
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40486081..40488912-chr21:40489931..40493675,3	K562	blood:
2	chr21:40480319..40482788-chr21:40486845..40488850,2	K562	blood:
3	chr21:40480995..40484748-chr21:40484754..40488551,5	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1013129	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1554930	0.82[MEX][hapmap]
rs1554931	0.81[MEX][hapmap]
rs1810383	0.83[ASN][1000 genomes]
rs1810384	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1882777	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2142112	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2836895	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs373728	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs375073	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431284	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs431376	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431704	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs442916	0.87[ASN][1000 genomes]
rs7283826	0.83[ASN][1000 genomes]
rs8128678	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs909181	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs941385	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9974464	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs454902	RCAN1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40478600-40497000	Weak transcription	Right Atrium	heart
2	chr21:40483200-40487000	Weak transcription	Lung	lung
3	chr21:40483200-40488000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr21:40485000-40487000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr21:40485200-40487600	Enhancers	K562	blood
6	chr21:40485400-40487000	Weak transcription	Fetal Stomach	stomach
7	chr21:40485600-40487200	Weak transcription	Fetal Lung	lung
8	chr21:40485800-40487200	Enhancers	Aorta	Aorta
9	chr21:40486000-40487200	Enhancers	Fetal Brain Male	brain
10	chr21:40486000-40487200	Enhancers	NHDF-Ad	bronchial
11	chr21:40486000-40488000	Enhancers	NH-A	brain
12	chr21:40486200-40487400	Enhancers	Placenta	Placenta
13	chr21:40486200-40487800	Enhancers	Psoas Muscle	Psoas
14	chr21:40486200-40487800	Enhancers	Osteobl	bone
15	chr21:40486400-40487200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:40486400-40487200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr21:40486400-40487200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr21:40486400-40487600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr21:40486400-40487600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr21:40486400-40487800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr21:40486400-40487800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr21:40486400-40488000	Enhancers	HepG2	liver
23	chr21:40486600-40487000	Enhancers	HSMM	muscle
24	chr21:40486600-40487200	Enhancers	HMEC	breast
25	chr21:40486600-40487400	Enhancers	A549	lung
26	chr21:40486600-40487600	Enhancers	Fetal Muscle Leg	muscle
27	chr21:40486600-40487600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr21:40486600-40487800	Enhancers	NHLF	lung
29	chr21:40486600-40488000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr21:40486600-40488000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr21:40486600-40497800	Weak transcription	Thymus	Thymus
32	chr21:40486800-40487200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
33	chr21:40486800-40487400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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