Variant report

Variant	rs331142
Chromosome Location	chr3:78920844-78920845
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78917265..78919312-chr3:78919747..78921686,2	MCF-7	breast:
2	chr3:78917237..78919813-chr3:78920275..78923386,3	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11127635	0.90[CEU][hapmap]
rs17016554	0.81[CEU][hapmap]
rs182796	0.88[EUR][1000 genomes]
rs331144	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331146	1.00[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.94[EUR][1000 genomes]
rs331147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856695	0.90[CEU][hapmap]
rs6770639	0.85[CEU][hapmap]

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	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs331142	FGF10	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78916200-78923000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:78916400-78921400	Enhancers	HepG2	liver
3	chr3:78917000-78921000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:78917400-78921200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:78917400-78921200	Weak transcription	Fetal Brain Male	brain
6	chr3:78917400-78921200	Weak transcription	Fetal Kidney	kidney
7	chr3:78917400-78921400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:78917400-78927000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:78917600-78924400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:78918000-78921200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:78918000-78921200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:78918000-78921400	Weak transcription	Brain Germinal Matrix	brain
13	chr3:78918000-78921400	Weak transcription	Fetal Lung	lung
14	chr3:78918000-78924800	Weak transcription	NHDF-Ad	bronchial
15	chr3:78918000-78928800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:78918000-78929800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:78918800-78921000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:78918800-78921400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:78918800-78927400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:78919200-78923400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:78919400-78921800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr3:78919400-78922200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:78919400-78923000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:78919600-78921000	Enhancers	A549	lung
25	chr3:78919600-78921400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr3:78919800-78921000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:78919800-78921400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:78919800-78922200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:78919800-78923000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:78920000-78921200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:78920000-78921200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:78920000-78921400	Weak transcription	Brain Angular Gyrus	brain
33	chr3:78920000-78921400	Weak transcription	Brain Anterior Caudate	brain
34	chr3:78920000-78922800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:78920000-78924800	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:78920200-78921000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr3:78920200-78921400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr3:78920200-78923000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:78920400-78921200	Weak transcription	Brain Substantia Nigra	brain
40	chr3:78920400-78923200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:78920400-78927000	Weak transcription	Aorta	Aorta
42	chr3:78920600-78922000	Enhancers	NH-A	brain
43	chr3:78920800-78924600	Weak transcription	Osteobl	bone
44	chr3:78920800-78927000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links