Variant report

Variant	rs57422239
Chromosome Location	chr15:62344569-62344570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:62343215..62348016-chr15:62348672..62353157,7	K562	blood:
2	chr15:62343402..62345177-chr15:62352458..62354579,2	MCF-7	breast:
3	chr15:62344281..62348307-chr15:62349170..62353134,6	K562	blood:

Variant related genes	Relation type
ENSG00000129003	Chromatin interaction
ENSG00000259251	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs13329329	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13329639	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17238245	0.89[EUR][1000 genomes]
rs17238301	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17303989	0.89[EUR][1000 genomes]
rs28367150	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28403096	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28408506	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28411845	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28440175	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28493143	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28517433	0.96[ASN][1000 genomes]
rs28541511	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28583709	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613580	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28650099	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28654580	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28664955	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28692770	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28708564	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28718088	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28720854	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28721460	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28758709	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28783433	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28810829	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28814609	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3784631	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4774423	0.83[EUR][1000 genomes]
rs725174	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73414700	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73416527	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73416547	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73430416	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8027343	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040911	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8042267	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9920006	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9920015	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920256	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9920390	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9920581	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
2	chr15:62276400-62345000	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:62300400-62351400	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:62300600-62345800	Weak transcription	Gastric	stomach
5	chr15:62300600-62351800	Weak transcription	Lung	lung
6	chr15:62300800-62351600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:62302200-62351600	Weak transcription	Fetal Thymus	thymus
8	chr15:62302200-62351600	Weak transcription	Ovary	ovary
9	chr15:62313400-62345600	Weak transcription	Brain Anterior Caudate	brain
10	chr15:62321200-62350800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:62328000-62345800	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:62328000-62350000	Weak transcription	Brain Angular Gyrus	brain
13	chr15:62328200-62350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:62328400-62350800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:62328400-62351200	Weak transcription	NHLF	lung
16	chr15:62328400-62351400	Weak transcription	Osteobl	bone
17	chr15:62328600-62345000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:62328800-62350000	Weak transcription	HUVEC	blood vessel
19	chr15:62328800-62350800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:62329000-62350400	Weak transcription	NHDF-Ad	bronchial
21	chr15:62330800-62348600	Weak transcription	Fetal Intestine Small	intestine
22	chr15:62332600-62345400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:62333400-62351400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:62333600-62345400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr15:62333600-62351400	Weak transcription	HSMM	muscle
26	chr15:62333800-62350600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:62334400-62345000	Weak transcription	Dnd41	blood
28	chr15:62335000-62345400	Weak transcription	Liver	Liver
29	chr15:62336000-62350400	Weak transcription	Fetal Intestine Large	intestine
30	chr15:62338800-62345600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:62338800-62345800	Weak transcription	Primary T cells from cord blood	blood
32	chr15:62339600-62345800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:62339600-62350800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:62340000-62345000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr15:62340000-62345000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:62340000-62345000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:62340000-62345000	Weak transcription	Adipose Nuclei	Adipose
38	chr15:62340200-62344800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr15:62340200-62345000	Weak transcription	Primary B cells from cord blood	blood
40	chr15:62340200-62345000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:62340200-62345000	Weak transcription	GM12878-XiMat	blood
42	chr15:62340200-62346000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr15:62342200-62351400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr15:62342400-62344800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr15:62342600-62347600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr15:62342800-62345000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:62342800-62345000	Weak transcription	Stomach Mucosa	stomach
48	chr15:62343000-62345600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:62343000-62345800	Weak transcription	Right Atrium	heart
50	chr15:62343000-62350600	Weak transcription	K562	blood

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