Variant report

Variant	rs6029969
Chromosome Location	chr20:40727031-40727032
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: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs56165650	1.00[AMR][1000 genomes]
rs57040102	0.83[AMR][1000 genomes]
rs58841508	0.93[AFR][1000 genomes]
rs6016681	0.93[AFR][1000 genomes]
rs6016682	0.93[AFR][1000 genomes]
rs6016683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6016684	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6029961	0.85[AMR][1000 genomes]
rs6029962	1.00[AMR][1000 genomes]
rs6029963	0.89[AFR][1000 genomes]
rs6029964	0.84[AFR][1000 genomes]
rs6029966	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6029967	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6029968	1.00[MEX][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6029970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6029971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6029973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6029977	1.00[AMR][1000 genomes]
rs6029978	1.00[AMR][1000 genomes]
rs6030031	1.00[MEX][hapmap]
rs61122863	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6513765	0.93[AFR][1000 genomes]
rs7266940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73129186	0.93[AFR][1000 genomes]
rs7347140	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs73907081	0.85[AMR][1000 genomes]
rs73907101	1.00[AMR][1000 genomes]
rs73909211	1.00[AMR][1000 genomes]
rs8123173	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8123284	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8123286	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8124637	0.93[AFR][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:12 , 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	chr20:40726000-40727800	Enhancers	Brain Germinal Matrix	brain
10	chr20:40726000-40727800	Enhancers	Duodenum Mucosa	Duodenum
11	chr20:40726800-40727400	Enhancers	Fetal Brain Female	brain
12	chr20:40727000-40729600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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