Variant report

Variant	rs9475054
Chromosome Location	chr6:54740541-54740542
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54736804..54741584-chr6:54742863..54746409,5	MCF-7	breast:
2	chr6:54704497..54716767-chr6:54728797..54750947,71	MCF-7	breast:
3	chr6:54594451..54596147-chr6:54739921..54742591,2	MCF-7	breast:
4	chr6:54560857..54562671-chr6:54739251..54742148,2	MCF-7	breast:
5	chr6:54564170..54566593-chr6:54739128..54740974,2	MCF-7	breast:
6	chr6:54585487..54587893-chr6:54738565..54741108,3	MCF-7	breast:
7	chr6:54589905..54593836-chr6:54739903..54743144,4	MCF-7	breast:
8	chr6:54740124..54741737-chr6:55103503..55105754,2	MCF-7	breast:
9	chr6:54722087..54723804-chr6:54738855..54741615,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224984	Chromatin interaction
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs9464154	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9464157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9464163	1.00[AMR][1000 genomes]
rs9475050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475067	1.00[AMR][1000 genomes]
rs9475072	1.00[AMR][1000 genomes]
rs9475073	1.00[AMR][1000 genomes]
rs9475126	1.00[AMR][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:21 , 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	chr6:54734600-54741800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:54736800-54741800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:54737200-54742200	Enhancers	HMEC	breast
7	chr6:54737200-54746400	Enhancers	Hela-S3	cervix
8	chr6:54737600-54755800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:54737800-54740800	Enhancers	NHEK	skin
10	chr6:54739200-54741400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:54739400-54741600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:54739400-54742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:54739400-54742600	Weak transcription	Stomach Mucosa	stomach
14	chr6:54739800-54742000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
16	chr6:54740000-54741800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:54740000-54742400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:54740200-54741800	Weak transcription	Fetal Intestine Large	intestine
19	chr6:54740200-54742000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:54740400-54740600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:54740400-54740800	Enhancers	Rectal Mucosa Donor 31	rectum

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