Variant report

Variant	rs4726467
Chromosome Location	chr7:139637422-139637423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:139636566..139639672-chr7:139642737..139644709,4	K562	blood:
2	chr7:139636456..139638180-chr7:139647527..139649483,2	K562	blood:
3	chr7:139635222..139637429-chr7:139651443..139653383,2	MCF-7	breast:
4	chr7:139636566..139638144-chr7:139641921..139644709,2	K562	blood:
5	chr7:139611287..139613050-chr7:139636783..139638353,2	K562	blood:
6	chr7:139476437..139478390-chr7:139635969..139638135,2	K562	blood:

Variant related genes	Relation type
ENSG00000059377	Chromatin interaction
ENSG00000064393	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16934	1.00[MEX][hapmap]
rs4726456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6952940	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription 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	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv831156	chr7:139532318-139694326	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1019001	chr7:139558216-139841268	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1029099	chr7:139558216-139869148	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv889245	chr7:139599229-139657221	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4726467	SNORD29	trans	lymphoblastoid	seeQTL
rs4726467	FOXA1	trans	lymphoblastoid	seeQTL
rs4726467	SAGE1	trans	lymphoblastoid	seeQTL
rs4726467	MIR630	trans	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139615400-139645000	Weak transcription	Primary T cells from cord blood	blood
2	chr7:139618600-139644800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:139634000-139656800	Weak transcription	Thymus	Thymus
4	chr7:139634200-139642200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:139635600-139637600	Strong transcription	Lung	lung
6	chr7:139635600-139637800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr7:139636000-139638800	Enhancers	K562	blood
8	chr7:139636200-139637600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:139636200-139638200	Enhancers	Placenta	Placenta
10	chr7:139636200-139640200	Genic enhancers	Primary monocytes fromperipheralblood	blood
11	chr7:139636400-139637600	Enhancers	HUVEC	blood vessel
12	chr7:139636600-139637600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr7:139636600-139637800	Enhancers	Fetal Muscle Leg	muscle
14	chr7:139636600-139639400	Enhancers	Primary hematopoietic stem cells	blood
15	chr7:139636600-139639600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:139636800-139637800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:139636800-139638200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr7:139636800-139638600	Enhancers	Primary B cells from cord blood	blood
19	chr7:139636800-139638600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:139636800-139645400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr7:139636800-139645400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:139637000-139637600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr7:139637000-139638200	Enhancers	Adipose Nuclei	Adipose
24	chr7:139637000-139638600	Genic enhancers	Fetal Thymus	thymus
25	chr7:139637000-139639400	Weak transcription	Spleen	Spleen
26	chr7:139637200-139637600	Enhancers	Brain Cingulate Gyrus	brain
27	chr7:139637200-139638200	Enhancers	Duodenum Mucosa	Duodenum
28	chr7:139637200-139638200	Weak transcription	Stomach Mucosa	stomach
29	chr7:139637200-139638200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
30	chr7:139637200-139638400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:139637200-139638600	Enhancers	Primary B cells from peripheral blood	blood
32	chr7:139637400-139637600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr7:139637400-139637800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:139637400-139638000	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
35	chr7:139637400-139638200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:139637400-139638200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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