Variant report

Variant	rs1278942
Chromosome Location	chr14:32419331-32419332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:32415369..32417109-chr14:32417144..32419896,2	MCF-7	breast:
2	chr14:32412347..32415225-chr14:32417011..32419996,3	MCF-7	breast:
3	chr14:32418462..32421329-chr14:32545887..32548430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258474	Chromatin interaction
ENSG00000258655	Chromatin interaction
ENSG00000100852	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1278931	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1278933	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1278934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1278935	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1278936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1278937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1278938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1278939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1278940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1278941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1278943	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1756720	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1761072	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1761076	0.98[ASN][1000 genomes]
rs2236532	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv564182	chr14:32110519-32584337	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046526	chr14:32110537-32567426	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv526200	chr14:32308511-32454372	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1278942	BAZ1A	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:32407400-32419800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr14:32412400-32419600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:32412800-32419800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr14:32413000-32419600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr14:32413400-32420800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr14:32413600-32420600	Enhancers	HMEC	breast
7	chr14:32413800-32420800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr14:32414400-32419400	Weak transcription	Brain Germinal Matrix	brain
9	chr14:32414600-32419400	Weak transcription	Fetal Muscle Leg	muscle
10	chr14:32414600-32419600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr14:32414600-32419600	Weak transcription	Adipose Nuclei	Adipose
12	chr14:32414600-32419600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr14:32414600-32419600	Weak transcription	Left Ventricle	heart
14	chr14:32414600-32419600	Weak transcription	Right Atrium	heart
15	chr14:32414600-32419800	Weak transcription	Gastric	stomach
16	chr14:32414600-32419800	Weak transcription	Lung	lung
17	chr14:32414600-32419800	Weak transcription	Psoas Muscle	Psoas
18	chr14:32414600-32420000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr14:32414800-32420000	Weak transcription	Pancreas	Pancrea
20	chr14:32415200-32419600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr14:32415600-32419600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr14:32415800-32419800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr14:32416800-32420600	Enhancers	NHEK	skin
24	chr14:32417600-32419800	Weak transcription	Right Ventricle	heart
25	chr14:32418400-32420800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr14:32418400-32422000	Enhancers	Placenta	Placenta
27	chr14:32418600-32419600	Enhancers	Hela-S3	cervix
28	chr14:32418600-32420800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:32418600-32420800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr14:32418600-32420800	Enhancers	NHDF-Ad	bronchial
31	chr14:32418800-32420000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr14:32418800-32420600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr14:32418800-32420600	Flanking Active TSS	A549	lung
34	chr14:32418800-32420800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:32418800-32421000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr14:32418800-32421000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr14:32418800-32421000	Enhancers	HSMMtube	muscle
38	chr14:32418800-32421200	Enhancers	Fetal Intestine Large	intestine
39	chr14:32418800-32421400	Enhancers	Stomach Mucosa	stomach
40	chr14:32418800-32422000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr14:32418800-32422000	Enhancers	Fetal Stomach	stomach
42	chr14:32418800-32422400	Enhancers	K562	blood
43	chr14:32418800-32423600	Enhancers	Fetal Lung	lung
44	chr14:32419000-32419400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr14:32419000-32419400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr14:32419000-32419400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr14:32419000-32419600	Weak transcription	NH-A	brain
48	chr14:32419000-32420000	Enhancers	Fetal Kidney	kidney
49	chr14:32419000-32420000	Enhancers	HUVEC	blood vessel
50	chr14:32419000-32420600	Enhancers	Muscle Satellite Cultured Cells	--

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