Variant report

Variant	rs56870093
Chromosome Location	chr10:5625436-5625437
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5612848..5615764-chr10:5625126..5626757,2	K562	blood:
2	chr10:5541034..5543833-chr10:5624036..5628974,4	MCF-7	breast:
3	chr10:5624309..5631245-chr10:5648674..5654250,8	MCF-7	breast:
4	chr10:5623673..5635207-chr10:5656121..5669428,27	MCF-7	breast:
5	chr10:5624223..5628705-chr10:5705947..5708974,4	MCF-7	breast:
6	chr10:5623488..5628108-chr10:5662504..5666628,7	MCF-7	breast:
7	chr10:5622553..5625678-chr10:5643794..5647662,4	MCF-7	breast:
8	chr10:5543933..5545635-chr10:5625422..5627089,2	MCF-7	breast:
9	chr10:5497463..5498986-chr10:5623708..5625714,2	MCF-7	breast:
10	chr10:5529211..5535200-chr10:5622519..5627906,7	MCF-7	breast:
11	chr10:5624520..5626694-chr10:5651576..5653939,2	K562	blood:
12	chr10:5624590..5636573-chr10:5652742..5661113,15	MCF-7	breast:
13	chr10:5584975..5598212-chr10:5621607..5634806,86	MCF-7	breast:
14	chr10:5486586..5497147-chr10:5622068..5633259,25	MCF-7	breast:
15	chr10:5482726..5485954-chr10:5624615..5627364,3	MCF-7	breast:

No data

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

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

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

rs_ID	r²[population]
rs4881481	0.85[ASN][1000 genomes]
rs55794432	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55915230	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56019774	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56052209	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56113508	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56172763	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56197874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56280752	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58411480	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58589352	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60208988	0.84[EUR][1000 genomes]
rs61628927	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7898549	0.89[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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5623000-5626600	Enhancers	Primary B cells from peripheral blood	blood
2	chr10:5623200-5626200	Enhancers	Primary B cells from cord blood	blood
3	chr10:5623800-5625600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:5623800-5625800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:5623800-5626200	Flanking Active TSS	GM12878-XiMat	blood
6	chr10:5624000-5625600	Enhancers	HepG2	liver
7	chr10:5624000-5627400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:5624200-5625600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr10:5624200-5628200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:5624200-5630400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr10:5624400-5626000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr10:5624400-5626600	Weak transcription	Esophagus	oesophagus
13	chr10:5624400-5626600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr10:5624400-5627800	Enhancers	Placenta	Placenta
15	chr10:5624400-5628200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr10:5624400-5629400	Weak transcription	Colonic Mucosa	Colon
17	chr10:5624400-5629600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr10:5624600-5625600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:5624600-5625800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr10:5624600-5626200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr10:5624800-5625800	Weak transcription	Hela-S3	cervix
22	chr10:5624800-5627000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr10:5624800-5627600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr10:5625000-5625600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr10:5625000-5626200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr10:5625000-5631800	Weak transcription	K562	blood
27	chr10:5625000-5632400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr10:5625200-5626000	Enhancers	Brain Germinal Matrix	brain
29	chr10:5625200-5626000	Bivalent Enhancer	Fetal Thymus	thymus
30	chr10:5625200-5626200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:5625200-5626200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr10:5625200-5626200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
33	chr10:5625200-5626200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr10:5625200-5626400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:5625200-5626800	Enhancers	Duodenum Mucosa	Duodenum
36	chr10:5625200-5634400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:5625400-5625600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr10:5625400-5625600	Enhancers	Brain Anterior Caudate	brain
39	chr10:5625400-5625600	Enhancers	Fetal Heart	heart
40	chr10:5625400-5625600	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr10:5625400-5625600	Active TSS	Rectal Smooth Muscle	rectum
42	chr10:5625400-5625600	Enhancers	Right Atrium	heart
43	chr10:5625400-5625600	Enhancers	Right Ventricle	heart
44	chr10:5625400-5625600	Flanking Active TSS	HMEC	breast
45	chr10:5625400-5625800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:5625400-5625800	Enhancers	Fetal Muscle Leg	muscle
47	chr10:5625400-5625800	Weak transcription	Spleen	Spleen
48	chr10:5625400-5625800	Enhancers	NH-A	brain
49	chr10:5625400-5626000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr10:5625400-5626000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links