Variant report

Variant	rs55858643
Chromosome Location	chr15:56221055-56221056
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	chr15:56199193..56201528-chr15:56218643..56221076,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17238489	0.80[EUR][1000 genomes]
rs17819282	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819300	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2136386	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2175104	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55908996	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55999037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56109562	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56339902	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62043792	0.80[EUR][1000 genomes]
rs62043793	0.82[EUR][1000 genomes]
rs62043796	0.85[EUR][1000 genomes]
rs62043801	0.83[EUR][1000 genomes]
rs62043802	0.86[EUR][1000 genomes]
rs62043810	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62043815	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62043816	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62043847	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62043854	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62043858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62045161	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62045162	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62045163	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62045164	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62045205	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62045207	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62045208	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62045211	0.89[ASN][1000 genomes]
rs62045219	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62045225	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56190200-56221200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr15:56201000-56230000	Weak transcription	Fetal Intestine Large	intestine
3	chr15:56207600-56221200	Weak transcription	Right Ventricle	heart
4	chr15:56208800-56221600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:56208800-56230000	Weak transcription	Liver	Liver
6	chr15:56209000-56230400	Weak transcription	Primary T cells from cord blood	blood
7	chr15:56209200-56221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:56209200-56221600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:56209200-56230200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:56209200-56230200	Weak transcription	Aorta	Aorta
11	chr15:56209600-56230800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:56209600-56247400	Weak transcription	Psoas Muscle	Psoas
13	chr15:56210200-56221600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:56210200-56229600	Weak transcription	HSMMtube	muscle
15	chr15:56210200-56229800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:56210800-56228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:56210800-56229200	Weak transcription	HUVEC	blood vessel
18	chr15:56211000-56221200	Weak transcription	NHEK	skin
19	chr15:56211000-56221800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:56211400-56230800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:56211600-56229400	Weak transcription	A549	lung
22	chr15:56211800-56242400	Weak transcription	Hela-S3	cervix
23	chr15:56215000-56221200	Weak transcription	Thymus	Thymus
24	chr15:56216800-56230000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:56217200-56230000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:56218800-56230200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:56219200-56230200	Weak transcription	Fetal Intestine Small	intestine
28	chr15:56220800-56222400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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