Variant report

Variant	rs2425472
Chromosome Location	chr20:40726145-40726146
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	chr20:40704838..40706850-chr20:40726067..40728790,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1126102	0.83[EUR][1000 genomes]
rs1883375	0.93[ASN][1000 genomes]
rs1883380	0.80[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076247	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2143004	0.80[CHB][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2425467	0.86[EUR][1000 genomes]
rs2425469	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2425470	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2425471	0.94[ASN][1000 genomes]
rs2425473	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2425475	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2866942	0.89[ASN][1000 genomes]
rs2866947	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3091600	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3091875	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3091889	0.94[ASN][1000 genomes]
rs3091932	0.85[CHB][hapmap];0.80[JPT][hapmap];0.94[ASN][1000 genomes]
rs3092252	0.94[ASN][1000 genomes]
rs3092503	0.94[ASN][1000 genomes]
rs3092588	0.94[ASN][1000 genomes]
rs3092614	0.94[ASN][1000 genomes]
rs6130027	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7263976	0.85[CHB][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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

No data

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	chr20:40724800-40726800	Weak transcription	Fetal Brain Female	brain
8	chr20:40725200-40730800	Enhancers	Fetal Intestine Small	intestine
9	chr20:40725200-40731200	Enhancers	Fetal Intestine Large	intestine
10	chr20:40725800-40727000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr20:40726000-40727000	Enhancers	HepG2	liver
12	chr20:40726000-40727800	Enhancers	Brain Germinal Matrix	brain
13	chr20:40726000-40727800	Enhancers	Duodenum Mucosa	Duodenum

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