Variant report

Variant	rs4280164
Chromosome Location	chr14:24771285-24771286
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr14:24771047-24771555	SH-SY5Y	brain:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24702582..24706480-chr14:24770203..24773016,3	K562	blood:
2	chr14:24770771..24773074-chr14:24835790..24837584,2	MCF-7	breast:
3	chr14:24769506..24771314-chr14:24788379..24791495,3	K562	blood:
4	chr14:24769037..24771886-chr14:24904413..24906460,2	MCF-7	breast:
5	chr14:24701050..24707093-chr14:24765824..24771703,7	K562	blood:
6	chr14:24680927..24686311-chr14:24766466..24771455,6	K562	blood:
7	chr14:24682270..24687913-chr14:24764870..24771791,12	MCF-7	breast:
8	chr14:24655120..24666858-chr14:24765577..24776253,24	MCF-7	breast:
9	chr14:24767332..24771774-chr14:24910139..24913002,7	MCF-7	breast:
10	chr14:24767097..24775014-chr14:24779936..24787049,14	MCF-7	breast:
11	chr14:24766841..24768982-chr14:24770722..24773085,2	MCF-7	breast:
12	chr14:24740443..24742571-chr14:24769665..24772196,4	K562	blood:
13	chr14:24769087..24772179-chr14:24900488..24904117,5	K562	blood:
14	chr14:24768871..24772362-chr14:24798723..24803416,4	MCF-7	breast:
15	chr14:24740917..24742571-chr14:24770385..24772196,2	K562	blood:
16	chr14:24766804..24771569-chr14:24898237..24903800,5	MCF-7	breast:
17	chr14:24769018..24771644-chr14:24778129..24781269,3	K562	blood:

No data

Variant related genes	Relation type
NOP9	TF binding region
LTB4R2	TF binding region
DHRS1	TF binding region
ENSG00000213906	Chromatin interaction
ENSG00000136305	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000260669	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000259522	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000213920	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000272658	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000255526	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000100926	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000100938	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11158632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158634	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158635	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131941	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886362	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144494	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180196	0.90[GIH][hapmap];0.81[TSI][hapmap]
rs2224122	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224123	0.84[EUR][1000 genomes]
rs2281472	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2516564	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748543	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181384	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374085	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981503	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981504	0.85[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901499	chr14:24765622-24787588	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	n/a
4	nsv901500	chr14:24765622-24793762	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	n/a
5	nsv564058	chr14:24771285-24786976	Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
6	nsv901501	chr14:24771285-24793762	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Parent of origin effect on language impairment (paternal)	24571439	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4280164	NDRG2	cis	parietal	SCAN
rs4280164	ANG	cis	parietal	SCAN
rs4280164	TGM1	cis	cerebellum	SCAN
rs4280164	LTB4R	cis	Thyroid	GTEx
rs4280164	DHRS1	cis	parietal	SCAN
rs4280164	DHRS1	cis	cerebellum	SCAN
rs4280164	LRRC16B	cis	parietal	SCAN
rs4280164	NGDN	cis	parietal	SCAN
rs4280164	LTB4R	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24770000-24771400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:24770000-24773000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:24770200-24771400	Genic enhancers	Placenta	Placenta
4	chr14:24770200-24771400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr14:24770200-24772600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr14:24770200-24773000	Weak transcription	Psoas Muscle	Psoas
7	chr14:24770200-24777000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr14:24770200-24778600	Strong transcription	Fetal Stomach	stomach
9	chr14:24770200-24779400	Weak transcription	Right Atrium	heart
10	chr14:24770400-24771600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:24770400-24775400	Genic enhancers	Duodenum Mucosa	Duodenum
12	chr14:24770400-24775600	Genic enhancers	Liver	Liver
13	chr14:24770400-24775600	Genic enhancers	Fetal Intestine Small	intestine
14	chr14:24770400-24775800	Strong transcription	A549	lung
15	chr14:24770400-24777000	Strong transcription	Brain Cingulate Gyrus	brain
16	chr14:24770400-24778800	Weak transcription	Fetal Heart	heart
17	chr14:24770400-24782000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:24770600-24771600	Genic enhancers	Dnd41	blood
19	chr14:24770600-24775600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:24770600-24776200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:24770600-24776400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr14:24770600-24776400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr14:24770600-24776400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr14:24770600-24776400	Strong transcription	Fetal Thymus	thymus
25	chr14:24770600-24776600	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr14:24770600-24776600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr14:24770600-24776600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr14:24770600-24776800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr14:24770600-24776800	Strong transcription	Brain Germinal Matrix	brain
30	chr14:24770600-24777000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr14:24770600-24777000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr14:24770600-24777000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr14:24770600-24777000	Strong transcription	Ovary	ovary
34	chr14:24770600-24777000	Strong transcription	HMEC	breast
35	chr14:24770600-24777200	Strong transcription	Brain Hippocampus Middle	brain
36	chr14:24770600-24777200	Strong transcription	Fetal Muscle Leg	muscle
37	chr14:24770600-24777400	Strong transcription	Colon Smooth Muscle	Colon
38	chr14:24770600-24778000	Strong transcription	Thymus	Thymus
39	chr14:24770600-24781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:24770600-24781800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr14:24770800-24771400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr14:24770800-24771600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr14:24770800-24773000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr14:24770800-24773200	Strong transcription	Spleen	Spleen
45	chr14:24770800-24773400	Strong transcription	K562	blood
46	chr14:24770800-24773600	Strong transcription	NHDF-Ad	bronchial
47	chr14:24770800-24775200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr14:24770800-24775600	Strong transcription	Gastric	stomach
49	chr14:24770800-24775600	Strong transcription	Stomach Mucosa	stomach
50	chr14:24770800-24775600	Strong transcription	Osteobl	bone

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