Variant report

Variant	rs6554110
Chromosome Location	chr4:54413601-54413602
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54402473..54406249-chr4:54412987..54415087,4	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1435216	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1435217	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55823057	1.00[AMR][1000 genomes]
rs56388080	1.00[AMR][1000 genomes]
rs57155745	1.00[AMR][1000 genomes]
rs57685463	1.00[AMR][1000 genomes]
rs58208481	1.00[AMR][1000 genomes]
rs59232300	1.00[AMR][1000 genomes]
rs59761197	1.00[AMR][1000 genomes]
rs59961961	1.00[AMR][1000 genomes]
rs6554113	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6853185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6854868	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73145486	1.00[AMR][1000 genomes]
rs73145499	1.00[AMR][1000 genomes]
rs73147405	1.00[AMR][1000 genomes]
rs73818505	1.00[AMR][1000 genomes]
rs73818919	1.00[AMR][1000 genomes]
rs7681457	1.00[AMR][1000 genomes]
rs7695583	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs932038	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54374400-54421000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:54384600-54424000	Weak transcription	Esophagus	oesophagus
3	chr4:54390400-54430400	Weak transcription	Stomach Mucosa	stomach
4	chr4:54400400-54417000	Weak transcription	Fetal Intestine Small	intestine
5	chr4:54400600-54424400	Weak transcription	Fetal Intestine Large	intestine
6	chr4:54404200-54424400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:54404600-54419200	Weak transcription	Placenta	Placenta
8	chr4:54408600-54421000	Weak transcription	Brain Anterior Caudate	brain
9	chr4:54408800-54414000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:54408800-54420400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:54409000-54414000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:54409200-54427000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:54409400-54417400	Weak transcription	Right Atrium	heart
14	chr4:54409400-54420200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:54409600-54415000	Weak transcription	Fetal Brain Female	brain
16	chr4:54411200-54419200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:54411800-54413800	Enhancers	Liver	Liver
18	chr4:54412000-54413800	Enhancers	Pancreas	Pancrea
19	chr4:54412200-54414400	Enhancers	Aorta	Aorta
20	chr4:54412200-54442400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:54413200-54418000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:54413200-54418000	Weak transcription	NHDF-Ad	bronchial
23	chr4:54413200-54424000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:54413600-54413800	Enhancers	Right Ventricle	heart
25	chr4:54413600-54413800	Enhancers	Small Intestine	intestine
26	chr4:54413600-54414400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:54413600-54414400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr4:54413600-54414400	Enhancers	Left Ventricle	heart
29	chr4:54413600-54414800	Enhancers	HUVEC	blood vessel

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