Variant report

Variant	rs6554121
Chromosome Location	chr4:54509016-54509017
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54457408..54459119-chr4:54508678..54511662,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072201	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10005578	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10006267	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10010205	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10021678	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10027185	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027544	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10031525	0.97[ASN][1000 genomes]
rs10031866	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1039985	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12645402	0.88[ASN][1000 genomes]
rs13146347	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13148245	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1477878	0.87[ASN][1000 genomes]
rs1477880	0.86[ASN][1000 genomes]
rs17083218	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17083272	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17083277	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1991972	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991973	0.97[ASN][1000 genomes]
rs2086048	0.90[ASN][1000 genomes]
rs2219742	0.87[ASN][1000 genomes]
rs28678201	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3942650	0.97[ASN][1000 genomes]
rs4864809	1.00[ASN][1000 genomes]
rs6554120	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6816209	1.00[ASN][1000 genomes]
rs6818959	1.00[ASN][1000 genomes]
rs6843799	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6849381	0.88[ASN][1000 genomes]
rs6858782	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs750695	0.99[ASN][1000 genomes]
rs7688605	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54501400-54510800	Weak transcription	Right Atrium	heart
2	chr4:54506800-54511000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:54507200-54510000	Weak transcription	Small Intestine	intestine
4	chr4:54507200-54510600	Weak transcription	Placenta	Placenta
5	chr4:54507200-54511000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:54507400-54509800	Weak transcription	Pancreas	Pancrea
7	chr4:54507400-54510800	Weak transcription	Esophagus	oesophagus
8	chr4:54507400-54510800	Weak transcription	Left Ventricle	heart
9	chr4:54507400-54511400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:54507400-54511600	Weak transcription	Right Ventricle	heart
11	chr4:54507800-54509800	Weak transcription	Fetal Intestine Large	intestine
12	chr4:54507800-54509800	Weak transcription	Fetal Intestine Small	intestine
13	chr4:54507800-54510400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:54507800-54510400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:54507800-54510800	Weak transcription	Lung	lung
16	chr4:54507800-54510800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:54507800-54517000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:54507800-54520600	Weak transcription	Gastric	stomach
19	chr4:54508000-54511000	Weak transcription	Fetal Lung	lung
20	chr4:54508000-54512600	Weak transcription	Adipose Nuclei	Adipose
21	chr4:54508000-54519200	Weak transcription	Fetal Heart	heart
22	chr4:54508800-54510400	Weak transcription	GM12878-XiMat	blood
23	chr4:54509000-54511000	Enhancers	Stomach Mucosa	stomach

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