Variant report

Variant	rs6571547
Chromosome Location	chr14:33126382-33126383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:33121885..33124739-chr14:33125930..33128750,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10130459	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10135053	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10138218	0.81[AMR][1000 genomes]
rs1033678	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11625087	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12717222	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12896132	0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs1884618	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1956202	0.81[AMR][1000 genomes]
rs1956203	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1956219	0.83[AMR][1000 genomes]
rs3784203	0.81[AMR][1000 genomes]
rs4981992	0.90[GIH][hapmap]
rs4981995	0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6571540	0.83[GIH][hapmap]
rs6571548	1.00[CHB][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7146517	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7152044	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7153048	0.89[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7154753	0.83[AMR][1000 genomes]
rs7156763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7157328	0.84[AMR][1000 genomes]
rs7157533	0.93[GIH][hapmap];0.84[AMR][1000 genomes]
rs7157744	0.93[GIH][hapmap];0.84[AMR][1000 genomes]
rs7160156	0.97[GIH][hapmap]
rs927060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv1045035	chr14:32986003-33543227	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv542021	chr14:32986003-33543227	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv428624	chr14:33065571-33214223	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6571547	STRN3	cis	parietal	SCAN
rs6571547	NUBPL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:33107000-33130600	Weak transcription	Left Ventricle	heart
2	chr14:33113800-33130600	Weak transcription	Right Ventricle	heart
3	chr14:33115000-33134400	Weak transcription	Psoas Muscle	Psoas
4	chr14:33117800-33149200	Weak transcription	Colon Smooth Muscle	Colon
5	chr14:33120600-33128200	Weak transcription	Fetal Heart	heart
6	chr14:33121000-33134200	Weak transcription	Fetal Muscle Leg	muscle
7	chr14:33123600-33127400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr14:33125600-33126600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr14:33125600-33126800	Enhancers	Aorta	Aorta
10	chr14:33125600-33127400	Enhancers	Brain Anterior Caudate	brain
11	chr14:33125600-33127400	Enhancers	NHDF-Ad	bronchial
12	chr14:33125600-33127600	Enhancers	Brain Angular Gyrus	brain
13	chr14:33125800-33126600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr14:33125800-33126600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr14:33125800-33126800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr14:33125800-33126800	Enhancers	Brain Cingulate Gyrus	brain
17	chr14:33125800-33126800	Enhancers	HMEC	breast
18	chr14:33125800-33126800	Enhancers	NHLF	lung
19	chr14:33125800-33127400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr14:33125800-33127400	Enhancers	Brain Hippocampus Middle	brain
21	chr14:33125800-33127600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr14:33126000-33126600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr14:33126000-33126600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr14:33126000-33126800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr14:33126000-33126800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr14:33126000-33126800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr14:33126000-33126800	Flanking Active TSS	GM12878-XiMat	blood
28	chr14:33126000-33127400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr14:33126200-33126400	Enhancers	Adipose Nuclei	Adipose
30	chr14:33126200-33126400	Enhancers	Esophagus	oesophagus
31	chr14:33126200-33126600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr14:33126200-33126600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr14:33126200-33126600	Enhancers	K562	blood
34	chr14:33126200-33126800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:33126200-33126800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr14:33126200-33126800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr14:33126200-33126800	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr14:33126200-33126800	Enhancers	HSMM	muscle
39	chr14:33126200-33126800	Enhancers	HSMMtube	muscle
40	chr14:33126200-33127000	Enhancers	A549	lung
41	chr14:33126200-33127200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links