Variant report

Variant	rs3181384
Chromosome Location	chr14:24786976-24786977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:24785563..24788287-chr14:24805710..24808640,2	MCF-7	breast:
2	chr14:24654479..24657858-chr14:24783212..24786979,3	K562	blood:
3	chr14:24767097..24775014-chr14:24779936..24787049,14	MCF-7	breast:
4	chr14:24711592..24713123-chr14:24785220..24787593,2	K562	blood:
5	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
6	chr14:24786484..24789445-chr14:24867448..24869110,2	K562	blood:
7	chr14:24785903..24787847-chr14:24833580..24835158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139899	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000196943	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000213906	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000205978	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs11158632	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[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]
rs11158634	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158635	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131941	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886362	0.85[CEU][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144494	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180196	0.90[GIH][hapmap]
rs2224122	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224123	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2281472	0.93[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2516564	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2748543	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280164	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	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]
rs4374085	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981503	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981504	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	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
7	nsv564059	chr14:24776401-24796813	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv564060	chr14:24776401-24809795	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3181384	LRRC16B	cis	parietal	SCAN
rs3181384	ANG	cis	parietal	SCAN
rs3181384	TGM1	cis	cerebellum	SCAN
rs3181384	DHRS1	cis	cerebellum	SCAN
rs3181384	RABGGTA	cis	multi-tissue	Pritchard
rs3181384	NDRG2	cis	parietal	SCAN
rs3181384	LTB4R	cis	lung	GTEx
rs3181384	NGDN	cis	parietal	SCAN
rs3181384	LTB4R	cis	Thyroid	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24781200-24787200	Enhancers	HUVEC	blood vessel
2	chr14:24781800-24787600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:24783200-24788000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr14:24784000-24787600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr14:24784400-24787000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
6	chr14:24784600-24787200	Weak transcription	Primary T cells from cord blood	blood
7	chr14:24784600-24787200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr14:24784600-24787600	Enhancers	K562	blood
9	chr14:24784600-24796400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr14:24784800-24796600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr14:24785000-24789000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr14:24785200-24787200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr14:24785200-24787800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr14:24785200-24788800	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
15	chr14:24785400-24787200	Enhancers	HMEC	breast
16	chr14:24785400-24788000	Enhancers	Primary B cells from cord blood	blood
17	chr14:24785600-24787200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:24785600-24787200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr14:24785600-24787800	Enhancers	Primary hematopoietic stem cells	blood
20	chr14:24785800-24787200	Bivalent Enhancer	HepG2	liver
21	chr14:24785800-24787400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr14:24785800-24788000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr14:24786000-24787200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr14:24786000-24787200	Enhancers	Hela-S3	cervix
25	chr14:24786000-24787200	Enhancers	NHDF-Ad	bronchial
26	chr14:24786000-24787400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:24786200-24787000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:24786200-24787000	Enhancers	NHLF	lung
29	chr14:24786200-24787600	Weak transcription	Gastric	stomach
30	chr14:24786200-24801600	Weak transcription	Left Ventricle	heart
31	chr14:24786400-24787200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr14:24786400-24787200	Enhancers	A549	lung
33	chr14:24786400-24787200	Bivalent Enhancer	Osteobl	bone
34	chr14:24786400-24792200	Weak transcription	Esophagus	oesophagus
35	chr14:24786600-24787000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
36	chr14:24786600-24787000	Weak transcription	Spleen	Spleen
37	chr14:24786600-24787000	Bivalent Enhancer	NH-A	brain
38	chr14:24786600-24787200	Enhancers	NHEK	skin
39	chr14:24786800-24787000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr14:24786800-24787400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr14:24786800-24787600	Weak transcription	Adipose Nuclei	Adipose
42	chr14:24786800-24787800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr14:24786800-24788000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr14:24786800-24790800	Weak transcription	Lung	lung

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