Variant report

Variant	rs56252541
Chromosome Location	chr5:43532754-43532755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43527365..43529512-chr5:43530585..43533160,3	MCF-7	breast:
2	chr5:43522223..43525825-chr5:43531234..43533172,3	MCF-7	breast:
3	chr5:43523816..43525449-chr5:43531975..43533697,2	K562	blood:
4	chr5:43513716..43515768-chr5:43530681..43534102,3	K562	blood:
5	chr5:43531071..43533331-chr5:43556194..43557859,2	K562	blood:
6	chr5:43525503..43527779-chr5:43531737..43533752,2	K562	blood:

Variant related genes	Relation type
ENSG00000248240	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000172239	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10059912	0.82[ASN][1000 genomes]
rs10462051	0.82[ASN][1000 genomes]
rs12187908	0.84[ASN][1000 genomes]
rs12332560	0.82[ASN][1000 genomes]
rs12521249	0.82[ASN][1000 genomes]
rs12697457	0.82[ASN][1000 genomes]
rs13359906	0.82[ASN][1000 genomes]
rs28437972	0.82[ASN][1000 genomes]
rs4072918	0.82[ASN][1000 genomes]
rs4072919	0.82[ASN][1000 genomes]
rs4331909	0.82[ASN][1000 genomes]
rs4386738	0.82[ASN][1000 genomes]
rs4467713	0.82[ASN][1000 genomes]
rs4535459	0.82[ASN][1000 genomes]
rs4866830	0.91[ASN][1000 genomes]
rs4866831	0.86[ASN][1000 genomes]
rs4866833	0.82[ASN][1000 genomes]
rs4866835	0.82[ASN][1000 genomes]
rs55667604	0.82[ASN][1000 genomes]
rs55855322	0.82[ASN][1000 genomes]
rs56008952	0.80[ASN][1000 genomes]
rs59001943	0.82[ASN][1000 genomes]
rs60297702	0.82[ASN][1000 genomes]
rs6451712	0.82[ASN][1000 genomes]
rs67581152	0.80[ASN][1000 genomes]
rs6866325	0.82[ASN][1000 genomes]
rs6866802	0.82[ASN][1000 genomes]
rs6869933	0.82[ASN][1000 genomes]
rs6884661	0.82[ASN][1000 genomes]
rs6891363	0.82[ASN][1000 genomes]
rs72758674	0.93[ASN][1000 genomes]
rs7715782	0.80[ASN][1000 genomes]
rs7717636	0.82[ASN][1000 genomes]
rs7736615	0.80[ASN][1000 genomes]
rs9885189	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	esv1835057	chr5:43515280-43557405	Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	esv1835614	chr5:43515280-43561759	Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	esv1837000	chr5:43515280-43561759	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43515600-43533800	Weak transcription	Small Intestine	intestine
2	chr5:43515600-43534000	Weak transcription	Esophagus	oesophagus
3	chr5:43516000-43533800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:43516000-43534000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:43516200-43532800	Weak transcription	Fetal Heart	heart
6	chr5:43516200-43533600	Weak transcription	Brain Substantia Nigra	brain
7	chr5:43516200-43534200	Weak transcription	Stomach Mucosa	stomach
8	chr5:43516400-43534000	Weak transcription	Pancreas	Pancrea
9	chr5:43522200-43534000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:43523200-43550600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:43523200-43551600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:43523200-43551800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:43523200-43552200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:43523400-43551000	Strong transcription	Liver	Liver
15	chr5:43523400-43553600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:43523400-43554600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:43523600-43551000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr5:43523600-43554200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:43524000-43540200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:43524000-43555200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:43524200-43539600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:43524200-43553600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:43524600-43533800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:43524800-43553600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:43525000-43552400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:43525200-43548600	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr5:43525400-43553400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:43525600-43541800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:43526000-43533200	Weak transcription	Spleen	Spleen
30	chr5:43526000-43533800	Weak transcription	Right Ventricle	heart
31	chr5:43526000-43534000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:43526000-43534000	Weak transcription	Aorta	Aorta
33	chr5:43526000-43534000	Weak transcription	Gastric	stomach
34	chr5:43526000-43553200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:43526000-43554200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:43526200-43533600	Weak transcription	Brain Angular Gyrus	brain
37	chr5:43526600-43534000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:43527200-43538000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr5:43527200-43543400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:43527200-43543400	Strong transcription	Adipose Nuclei	Adipose
41	chr5:43527200-43548200	Strong transcription	HUVEC	blood vessel
42	chr5:43527200-43550400	Strong transcription	Dnd41	blood
43	chr5:43527200-43552000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:43527200-43552400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:43527400-43533800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:43527400-43552400	Strong transcription	Hela-S3	cervix
47	chr5:43527400-43554200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:43527600-43535800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:43527600-43537800	Strong transcription	NHDF-Ad	bronchial
50	chr5:43527600-43538000	Strong transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links