Variant report

Variant	rs1342457
Chromosome Location	chr10:90233649-90233650
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	chr10:90233064..90234940-chr11:69455221..69456769,2	MCF-7	breast:
2	chr10:90144173..90146300-chr10:90233140..90235508,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110092	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10509547	0.95[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10509548	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10509549	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10509550	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10736359	1.00[CEU][hapmap]
rs1169042	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11816967	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1325899	0.95[CEU][hapmap]
rs1325901	0.90[CEU][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1325904	1.00[CEU][hapmap];0.80[MEX][hapmap]
rs1359581	0.94[CEU][hapmap]
rs1359582	0.95[CEU][hapmap];0.80[MEX][hapmap]
rs1555839	0.80[CEU][hapmap];0.80[MEX][hapmap]
rs1573074	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17334741	0.82[CEU][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs17336288	0.95[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17426488	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1774977	0.82[CEU][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs1974053	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1980813	0.80[MEX][hapmap]
rs2437876	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs2477953	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2576158	1.00[CEU][hapmap]
rs2576162	0.95[CEU][hapmap];0.80[MEX][hapmap]
rs2576163	0.95[CEU][hapmap]
rs2576167	0.80[MEX][hapmap]
rs2576173	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2576175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2576177	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2765451	0.94[CEU][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2765453	0.95[CEU][hapmap]
rs2765457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57260181	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs792201	0.90[CEU][hapmap];0.89[AMR][1000 genomes]
rs792202	0.89[AMR][1000 genomes]
rs792203	0.89[AMR][1000 genomes]
rs792231	0.86[CEU][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 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	chr10:90227600-90237000	Weak transcription	Left Ventricle	heart
2	chr10:90228200-90234000	Weak transcription	Ovary	ovary
3	chr10:90228200-90234200	Weak transcription	Aorta	Aorta
4	chr10:90228600-90234000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr10:90228800-90234000	Weak transcription	Hela-S3	cervix
6	chr10:90229400-90234600	Weak transcription	Psoas Muscle	Psoas
7	chr10:90232400-90234600	Enhancers	HMEC	breast
8	chr10:90232600-90234200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr10:90232600-90234400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr10:90233000-90236000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:90233200-90234000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr10:90233400-90233800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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