Variant report

Variant	rs6878798
Chromosome Location	chr5:43549476-43549477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43547644..43550345-chr5:43550491..43552259,2	MCF-7	breast:
2	chr5:43490222..43492249-chr5:43547823..43550065,2	K562	blood:
3	chr5:43482801..43486073-chr5:43545843..43553223,8	K562	blood:

Variant related genes	Relation type
ENSG00000249492	Chromatin interaction
ENSG00000151881	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16873406	0.81[EUR][1000 genomes]
rs41271077	0.81[EUR][1000 genomes]
rs6863191	0.81[EUR][1000 genomes]
rs6873555	0.81[EUR][1000 genomes]
rs6890419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6896527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6896589	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7700826	0.81[EUR][1000 genomes]
rs7715976	1.00[EUR][1000 genomes]
rs7732357	0.85[EUR][1000 genomes]
rs9764227	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	esv3471239	chr5:43541792-43587904	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	esv3471240	chr5:43541792-43587904	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6878798	NNT	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43523200-43550600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:43523200-43551600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:43523200-43551800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:43523200-43552200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:43523400-43551000	Strong transcription	Liver	Liver
6	chr5:43523400-43553600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:43523400-43554600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:43523600-43551000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr5:43523600-43554200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:43524000-43555200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:43524200-43553600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:43524800-43553600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:43525000-43552400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:43525400-43553400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:43526000-43553200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:43526000-43554200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:43527200-43550400	Strong transcription	Dnd41	blood
18	chr5:43527200-43552000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:43527200-43552400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:43527400-43552400	Strong transcription	Hela-S3	cervix
21	chr5:43527400-43554200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:43527600-43550400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:43527600-43550800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:43527600-43550800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:43527600-43553200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:43527600-43554400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:43527600-43555600	Strong transcription	Fetal Thymus	thymus
28	chr5:43527600-43556000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:43527800-43552400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:43528000-43554800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:43530200-43552000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:43532200-43552200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr5:43532800-43552400	Strong transcription	Fetal Intestine Large	intestine
34	chr5:43532800-43554000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr5:43533000-43551400	Strong transcription	Fetal Lung	lung
36	chr5:43534200-43550600	Weak transcription	Fetal Heart	heart
37	chr5:43534400-43550400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:43534600-43554400	Weak transcription	Aorta	Aorta
39	chr5:43534800-43551200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr5:43534800-43554000	Weak transcription	Right Ventricle	heart
41	chr5:43535000-43553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:43537800-43549800	Strong transcription	Fetal Muscle Leg	muscle
43	chr5:43538000-43553600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:43538200-43550600	Strong transcription	Fetal Brain Female	brain
45	chr5:43538800-43551600	Strong transcription	HepG2	liver
46	chr5:43538800-43554600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:43539800-43554200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:43540000-43552200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:43540400-43551000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr5:43540600-43551000	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links