Variant report

Variant	rs1859464
Chromosome Location	chr14:71287885-71287886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71287022..71288979-chr14:71420720..71423622,2	MCF-7	breast:
2	chr14:71274624..71277570-chr14:71286483..71288714,2	MCF-7	breast:
3	chr14:71287734..71288653-chr14:71422559..71423263,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction
ENSG00000259153	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10146964	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs11158881	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11621236	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11622104	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs11622788	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11622989	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs11623147	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11844844	0.84[ASN][1000 genomes]
rs12437113	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs12437247	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12880887	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap]
rs12897139	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108537	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17108539	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17108548	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs17108555	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34509410	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34548271	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829955	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs67164415	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71425385	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7144786	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs7153601	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap]
rs731571	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8014624	0.86[CHB][hapmap]
rs8019156	0.81[CHB][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	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1859464	ADAM20	cis	cerebellum	SCAN
rs1859464	ACOT4	cis	cerebellum	SCAN
rs1859464	SLC8A3	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71277200-71288000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr14:71277200-71288400	Weak transcription	Pancreas	Pancrea
3	chr14:71277800-71288000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr14:71279400-71288000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr14:71282800-71288400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:71284400-71288000	Weak transcription	Psoas Muscle	Psoas
7	chr14:71284400-71288200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:71284400-71288200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr14:71284800-71288000	Weak transcription	A549	lung
10	chr14:71284800-71288200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:71285000-71288200	Weak transcription	GM12878-XiMat	blood
12	chr14:71285000-71288800	Weak transcription	Hela-S3	cervix
13	chr14:71285200-71288000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr14:71287400-71288200	Enhancers	Osteobl	bone
15	chr14:71287600-71288000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr14:71287600-71288000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr14:71287600-71288000	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr14:71287600-71288200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr14:71287600-71288200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:71287600-71288200	Enhancers	HMEC	breast
21	chr14:71287800-71288000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
22	chr14:71287800-71288000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr14:71287800-71288000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:71287800-71288000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
25	chr14:71287800-71288000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
26	chr14:71287800-71288000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
27	chr14:71287800-71288000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:71287800-71288000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr14:71287800-71288000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr14:71287800-71288000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr14:71287800-71288000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:71287800-71288000	Enhancers	Liver	Liver
33	chr14:71287800-71288000	Bivalent/Poised TSS	Dnd41	blood
34	chr14:71287800-71288000	Enhancers	HSMM	muscle
35	chr14:71287800-71288200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
36	chr14:71287800-71288200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
37	chr14:71287800-71288200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr14:71287800-71288200	Enhancers	NHEK	skin
39	chr14:71287800-71288400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr14:71287800-71288400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
41	chr14:71287800-71289800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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