Variant report

Variant	rs469353
Chromosome Location	chr21:40219058-40219059
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40218988..40223370-chr21:40223471..40227627,7	K562	blood:
2	chr21:40176403..40178101-chr21:40218059..40219647,2	K562	blood:
3	chr21:40176601..40179515-chr21:40218059..40219886,2	K562	blood:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1534824	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1534825	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1534826	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836696	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2836698	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2836699	0.90[ASN][1000 genomes]
rs2836701	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836702	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836705	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836706	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836708	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836709	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs457705	0.82[MEX][hapmap]
rs460475	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs461155	0.82[MEX][hapmap]
rs462776	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs463452	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs467940	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs467985	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs468094	0.83[ASN][1000 genomes]
rs468107	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs468193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs468331	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs468456	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs468529	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs468837	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs468849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs469180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs469303	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7276587	0.89[ASN][1000 genomes]
rs7279564	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7283959	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs469353	NDUFB2	trans	cerebellum	SCAN
rs469353	MX1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40196400-40229000	Weak transcription	Right Ventricle	heart
2	chr21:40203800-40225200	Weak transcription	Psoas Muscle	Psoas
3	chr21:40213000-40219200	Weak transcription	Right Atrium	heart
4	chr21:40213800-40219200	Weak transcription	Hela-S3	cervix
5	chr21:40214400-40219200	Weak transcription	Fetal Stomach	stomach
6	chr21:40215800-40219400	Weak transcription	NH-A	brain
7	chr21:40216000-40219200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:40216400-40219400	Weak transcription	HSMMtube	muscle
9	chr21:40216400-40221200	Weak transcription	HUVEC	blood vessel
10	chr21:40216600-40219200	Weak transcription	HMEC	breast
11	chr21:40216600-40219400	Weak transcription	NHDF-Ad	bronchial
12	chr21:40216800-40219200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr21:40216800-40219200	Weak transcription	Osteobl	bone
14	chr21:40217200-40219200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr21:40219000-40219400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr21:40219000-40219400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr21:40219000-40219800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr21:40219000-40220400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr21:40219000-40220400	Enhancers	NHEK	skin

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