Variant report

Variant	rs56205728
Chromosome Location	chr15:40567237-40567238
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:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40531660..40532193-chr15:40566578..40567313,2	MCF-7	breast:
2	chr15:40566616..40567536-chr15:40575443..40576329,2	K562	blood:
3	chr15:40078495..40079355-chr15:40566600..40567596,4	K562	blood:
4	chr15:40556498..40560954-chr15:40561713..40567483,5	MCF-7	breast:
5	chr15:39977990..39978884-chr15:40566769..40567521,2	K562	blood:
6	chr15:40531032..40531701-chr15:40566512..40567430,2	MCF-7	breast:
7	chr15:40513371..40515548-chr15:40567016..40569593,2	K562	blood:
8	chr15:40567195..40571331-chr15:40615416..40618233,4	K562	blood:
9	chr15:40337054..40338155-chr15:40566547..40567480,5	MCF-7	breast:
10	chr15:40543324..40544589-chr15:40566509..40567486,5	MCF-7	breast:
11	chr15:40509342..40510064-chr15:40566620..40567261,2	MCF-7	breast:
12	chr15:40078638..40079472-chr15:40566591..40567310,2	MCF-7	breast:
13	chr15:40336630..40337966-chr15:40566528..40567460,17	K562	blood:
14	chr15:40537059..40538375-chr15:40566657..40567392,4	MCF-7	breast:
15	chr15:40336985..40337912-chr15:40566972..40567506,2	MCF-7	breast:
16	chr15:40566814..40567330-chr15:40628604..40629206,2	K562	blood:
17	chr15:40567044..40569798-chr15:40602403..40604424,2	K562	blood:
18	chr15:40508806..40511063-chr15:40566498..40567957,44	K562	blood:
19	chr15:40537194..40537865-chr15:40566649..40567440,2	MCF-7	breast:
20	chr15:40509026..40510811-chr15:40564171..40567983,79	MCF-7	breast:
21	chr15:40507899..40511190-chr15:40564977..40567533,3	MCF-7	breast:
22	chr15:40566645..40567517-chr15:40601865..40602542,3	K562	blood:
23	chr15:40322252..40323110-chr15:40566583..40567527,5	K562	blood:
24	chr15:40508840..40510209-chr15:40566468..40567517,20	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128829	Chromatin interaction
ENSG00000259330	Chromatin interaction
ENSG00000259288	Chromatin interaction
ENSG00000137843	Chromatin interaction
ENSG00000156970	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs28676999	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56282503	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv904096	chr15:40550149-40604777	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv904097	chr15:40555065-40595627	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv517541	chr15:40557268-40595627	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv904098	chr15:40564576-40586537	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv457118	chr15:40565705-40606484	Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv569227	chr15:40565705-40606484	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	25056061	GWAS catalog

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40546000-40571800	Weak transcription	Right Ventricle	heart
2	chr15:40546200-40568200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:40550000-40568000	Weak transcription	Spleen	Spleen
4	chr15:40551400-40571000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:40553800-40570400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:40556200-40567400	Strong transcription	Fetal Intestine Small	intestine
7	chr15:40556200-40567600	Weak transcription	Colonic Mucosa	Colon
8	chr15:40557000-40568200	Weak transcription	Lung	lung
9	chr15:40557200-40571800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:40559000-40570000	Weak transcription	Brain Anterior Caudate	brain
11	chr15:40559200-40568000	Weak transcription	Brain Germinal Matrix	brain
12	chr15:40559200-40570000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:40559400-40570200	Weak transcription	Brain Angular Gyrus	brain
14	chr15:40559400-40571600	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:40559600-40568800	Weak transcription	Fetal Brain Female	brain
16	chr15:40559600-40569000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:40559600-40569200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:40559600-40570000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:40559600-40570400	Strong transcription	Esophagus	oesophagus
20	chr15:40559600-40571800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:40560200-40568200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:40560800-40571800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:40564400-40568000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:40564400-40569400	Strong transcription	NHEK	skin
25	chr15:40565600-40571800	Weak transcription	Right Atrium	heart
26	chr15:40566200-40570000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:40566400-40567400	Enhancers	Fetal Heart	heart
28	chr15:40566400-40567400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
29	chr15:40566400-40567800	Weak transcription	Placenta	Placenta
30	chr15:40566400-40571800	Weak transcription	Gastric	stomach
31	chr15:40566600-40567400	Enhancers	Primary T cells fromperipheralblood	blood
32	chr15:40566600-40567400	Enhancers	K562	blood
33	chr15:40566600-40569200	Enhancers	Adipose Nuclei	Adipose
34	chr15:40566800-40567400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr15:40566800-40567400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr15:40566800-40567400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:40566800-40567400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:40566800-40567400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:40566800-40567600	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr15:40567000-40567400	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr15:40567000-40567600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:40567000-40568200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:40567000-40568200	Weak transcription	Pancreas	Pancrea
44	chr15:40567000-40569000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:40567000-40569600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:40567000-40569600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:40567000-40569800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:40567000-40569800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr15:40567000-40569800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:40567000-40570600	Weak transcription	Fetal Intestine Large	intestine

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