Variant report

Variant	rs57271459
Chromosome Location	chr6:54744361-54744362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54743634..54746094-chr6:54790131..54791842,2	MCF-7	breast:
2	chr6:54704497..54716767-chr6:54728797..54750947,71	MCF-7	breast:
3	chr6:54582713..54585752-chr6:54741876..54745709,4	MCF-7	breast:
4	chr6:54741459..54745147-chr6:54761074..54763520,3	MCF-7	breast:
5	chr6:54736804..54741584-chr6:54742863..54746409,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224984	Chromatin interaction
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1155750	1.00[ASN][1000 genomes]
rs1503137	1.00[ASN][1000 genomes]
rs16886072	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16886073	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16886088	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16886105	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910352	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41431945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56667985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56745332	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56804573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73437775	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73437777	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73437783	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73437784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73437785	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73437796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73439703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73439709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739951	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54727200-54748800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:54737200-54746400	Enhancers	Hela-S3	cervix
3	chr6:54737600-54755800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
5	chr6:54741600-54744600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:54741800-54744800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:54741800-54744800	Enhancers	Fetal Intestine Large	intestine
8	chr6:54742000-54744400	Enhancers	Duodenum Mucosa	Duodenum
9	chr6:54742400-54744600	Enhancers	Fetal Intestine Small	intestine
10	chr6:54742400-54744800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr6:54742600-54744600	Enhancers	Stomach Mucosa	stomach
12	chr6:54742600-54745200	Enhancers	HMEC	breast
13	chr6:54743000-54752000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:54743200-54744400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:54743400-54744400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:54743800-54744400	Enhancers	Pancreas	Pancrea
17	chr6:54744200-54744800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:54744200-54744800	Enhancers	NHEK	skin
19	chr6:54744200-54745000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:54744200-54757600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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