Variant report

Variant	rs62412659
Chromosome Location	chr6:54742389-54742390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54704497..54716767-chr6:54728797..54750947,71	MCF-7	breast:
2	chr6:54582146..54584053-chr6:54741073..54743084,2	MCF-7	breast:
3	chr6:54594451..54596147-chr6:54739921..54742591,2	MCF-7	breast:
4	chr6:54582713..54585752-chr6:54741876..54745709,4	MCF-7	breast:
5	chr6:54589905..54593836-chr6:54739903..54743144,4	MCF-7	breast:
6	chr6:54741459..54745147-chr6:54761074..54763520,3	MCF-7	breast:
7	chr6:54742187..54744014-chr6:54753985..54756805,2	MCF-7	breast:
8	chr6:54585158..54588149-chr6:54741239..54743201,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12175211	0.88[EUR][1000 genomes]
rs16886094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16886188	0.88[EUR][1000 genomes]
rs17682340	0.87[ASN][1000 genomes]
rs3813847	0.88[EUR][1000 genomes]
rs62412651	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62414960	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62414962	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62414963	0.88[EUR][1000 genomes]
rs62416516	0.88[EUR][1000 genomes]
rs62416519	0.88[EUR][1000 genomes]
rs62416520	0.88[EUR][1000 genomes]
rs62416521	0.88[EUR][1000 genomes]
rs9357821	0.88[EUR][1000 genomes]
rs9367598	0.88[EUR][1000 genomes]
rs9370338	0.88[EUR][1000 genomes]
rs9370339	0.88[EUR][1000 genomes]
rs9370340	0.88[EUR][1000 genomes]
rs9370341	0.83[EUR][1000 genomes]
rs9382401	0.88[EUR][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:22 , 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	chr6:54727400-54743800	Weak transcription	Pancreas	Pancrea
3	chr6:54730400-54743800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:54737200-54746400	Enhancers	Hela-S3	cervix
5	chr6:54737600-54755800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:54739400-54742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:54739400-54742600	Weak transcription	Stomach Mucosa	stomach
8	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
9	chr6:54740000-54742400	Weak transcription	Fetal Intestine Small	intestine
10	chr6:54740600-54743000	Weak transcription	Fetal Kidney	kidney
11	chr6:54740800-54742400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:54741400-54743200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:54741600-54744600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:54741800-54743000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:54741800-54743600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr6:54741800-54744800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:54741800-54744800	Enhancers	Fetal Intestine Large	intestine
18	chr6:54742000-54742800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:54742000-54744200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:54742000-54744400	Enhancers	Duodenum Mucosa	Duodenum
21	chr6:54742200-54742600	Genic enhancers	HMEC	breast
22	chr6:54742200-54742600	Strong transcription	NHEK	skin

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