Variant report

Variant	rs56172763
Chromosome Location	chr10:5627064-5627065
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:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5621478..5624080-chr10:5625841..5627746,2	K562	blood:
2	chr10:5625670..5627432-chr10:5629113..5631880,2	K562	blood:
3	chr10:5541034..5543833-chr10:5624036..5628974,4	MCF-7	breast:
4	chr10:5624309..5631245-chr10:5648674..5654250,8	MCF-7	breast:
5	chr10:5623673..5635207-chr10:5656121..5669428,27	MCF-7	breast:
6	chr10:5624223..5628705-chr10:5705947..5708974,4	MCF-7	breast:
7	chr10:5599218..5601467-chr10:5626638..5630611,4	MCF-7	breast:
8	chr10:5523297..5525984-chr10:5626929..5628566,2	MCF-7	breast:
9	chr10:5623488..5628108-chr10:5662504..5666628,7	MCF-7	breast:
10	chr10:5505541..5510842-chr10:5625752..5629034,6	MCF-7	breast:
11	chr10:5543933..5545635-chr10:5625422..5627089,2	MCF-7	breast:
12	chr10:5529211..5535200-chr10:5622519..5627906,7	MCF-7	breast:
13	chr10:5624590..5636573-chr10:5652742..5661113,15	MCF-7	breast:
14	chr10:5584975..5598212-chr10:5621607..5634806,86	MCF-7	breast:
15	chr10:5625746..5627987-chr10:5645084..5647138,2	MCF-7	breast:
16	chr10:5486586..5497147-chr10:5622068..5633259,25	MCF-7	breast:
17	chr10:5482726..5485954-chr10:5624615..5627364,3	MCF-7	breast:
18	chr10:5535730..5537593-chr10:5625752..5627612,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASB13-5	chr10:5626954-5627110	NONHSAT011162

No data

Variant related genes	Relation type
ENSG00000228685	Chromatin interaction
ENSG00000231483	Chromatin interaction
ENSG00000196372	Chromatin interaction
ENSG00000178372	Chromatin interaction
ENSG00000228951	Chromatin interaction
ENSG00000173848	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs55794432	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55915230	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56019774	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56052209	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56113508	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56197874	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56280752	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56870093	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58411480	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58589352	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60208988	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60839574	0.99[ASN][1000 genomes]
rs61628927	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898549	0.97[AMR][1000 genomes];0.93[EUR][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	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers 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	68 gene(s)	inside rSNPs	diseases
2	nsv932104	chr10:5203626-5641023	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv549886	chr10:5205437-5632060	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1054865	chr10:5225305-5638119	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv894798	chr10:5503610-5670275	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv523491	chr10:5542109-5720067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	esv2757364	chr10:5557024-5720512	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv894801	chr10:5600202-5631737	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv894802	chr10:5608202-5631737	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv549889	chr10:5610349-5630131	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5624000-5627400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:5624200-5628200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:5624200-5630400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr10:5624400-5627800	Enhancers	Placenta	Placenta
5	chr10:5624400-5628200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr10:5624400-5629400	Weak transcription	Colonic Mucosa	Colon
7	chr10:5624400-5629600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr10:5624800-5627600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr10:5625000-5631800	Weak transcription	K562	blood
10	chr10:5625000-5632400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr10:5625200-5634400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr10:5625400-5627800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:5625400-5628200	Enhancers	Fetal Lung	lung
14	chr10:5625400-5628400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:5625600-5627200	Weak transcription	Fetal Intestine Large	intestine
16	chr10:5625600-5629800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:5625800-5627600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:5625800-5628600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:5625800-5628800	Enhancers	Hela-S3	cervix
20	chr10:5625800-5629000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr10:5626000-5627400	Weak transcription	Brain Germinal Matrix	brain
22	chr10:5626000-5627800	Enhancers	Fetal Muscle Trunk	muscle
23	chr10:5626000-5629000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr10:5626000-5629800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr10:5626000-5634600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:5626200-5627200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:5626200-5627200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr10:5626200-5627200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:5626200-5627200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:5626200-5627200	Weak transcription	Fetal Brain Female	brain
31	chr10:5626200-5627200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr10:5626200-5627400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:5626200-5627600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr10:5626200-5627800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr10:5626200-5627800	Weak transcription	Stomach Mucosa	stomach
36	chr10:5626200-5628000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr10:5626200-5628200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr10:5626200-5628400	Weak transcription	Fetal Intestine Small	intestine
39	chr10:5626200-5628600	Enhancers	NHEK	skin
40	chr10:5626200-5628800	Enhancers	NH-A	brain
41	chr10:5626200-5629000	Weak transcription	Pancreas	Pancrea
42	chr10:5626200-5629200	Enhancers	HMEC	breast
43	chr10:5626200-5636200	Weak transcription	Primary B cells from cord blood	blood
44	chr10:5626400-5628200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:5626400-5628200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr10:5626400-5633600	Enhancers	Fetal Thymus	thymus
47	chr10:5626600-5627200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr10:5626600-5627400	Enhancers	Muscle Satellite Cultured Cells	--
49	chr10:5626600-5627600	Enhancers	Osteobl	bone
50	chr10:5626600-5627800	Enhancers	Esophagus	oesophagus

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