Variant report

Variant	rs1883375
Chromosome Location	chr20:40726827-40726828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:40704838..40706850-chr20:40726067..40728790,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1883380	0.93[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2076247	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2143004	0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2425469	0.93[ASN][1000 genomes]
rs2425470	0.90[ASN][1000 genomes]
rs2425471	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2425472	0.93[ASN][1000 genomes]
rs2425473	0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2425475	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2866942	0.85[ASN][1000 genomes]
rs2866947	0.90[ASN][1000 genomes]
rs3091600	0.93[ASN][1000 genomes]
rs3091875	0.91[ASN][1000 genomes]
rs3091889	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3091932	0.93[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3092252	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3092503	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3092588	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3092614	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6130027	0.87[ASN][1000 genomes]
rs7263976	0.85[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.85[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	nsv3381	chr20:39925326-40765696	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1883375	SNORA60	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40714600-40730000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr20:40715800-40757600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr20:40722400-40728400	Weak transcription	Pancreas	Pancrea
4	chr20:40722800-40747200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr20:40723000-40728600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr20:40723200-40741400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:40725200-40730800	Enhancers	Fetal Intestine Small	intestine
8	chr20:40725200-40731200	Enhancers	Fetal Intestine Large	intestine
9	chr20:40725800-40727000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr20:40726000-40727000	Enhancers	HepG2	liver
11	chr20:40726000-40727800	Enhancers	Brain Germinal Matrix	brain
12	chr20:40726000-40727800	Enhancers	Duodenum Mucosa	Duodenum
13	chr20:40726800-40727400	Enhancers	Fetal Brain Female	brain

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