Variant report

Variant	rs11070413
Chromosome Location	chr15:44218438-44218439
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:44218373-44218851	MCF-7	breast:	n/a	chr15:44218621-44218628 chr15:44218621-44218628 chr15:44218614-44218635 chr15:44218621-44218628

Variant related genes	Relation type
FRMD5	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1008183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10163054	0.82[GIH][hapmap]
rs1077421	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11070415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070416	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630936	1.00[CEU][hapmap];0.93[JPT][hapmap];0.84[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635039	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11637468	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12439442	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12440402	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16944774	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16945686	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs16950215	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2306674	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs28377221	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28438984	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28525216	1.00[TSI][hapmap]
rs28542819	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28599486	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28685813	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28706414	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3742981	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3850777	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55927923	0.97[EUR][1000 genomes]
rs60484809	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7167976	0.82[CHB][hapmap]
rs7178452	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9806129	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920164	1.00[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11070413	LOC440278	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44208800-44222600	Weak transcription	Fetal Brain Female	brain
2	chr15:44211800-44221800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:44211800-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:44212400-44220600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:44212400-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:44213400-44221600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:44213600-44219800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:44214000-44221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:44214000-44224400	Weak transcription	Right Atrium	heart
10	chr15:44214400-44224000	Weak transcription	HSMMtube	muscle
11	chr15:44215800-44221400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:44216400-44218600	Weak transcription	Brain Substantia Nigra	brain
13	chr15:44216400-44220600	Weak transcription	Brain Anterior Caudate	brain
14	chr15:44216600-44219800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:44216600-44222200	Weak transcription	NH-A	brain
16	chr15:44217600-44219600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr15:44217600-44219600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr15:44217600-44220200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:44217600-44220600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr15:44217800-44218800	Enhancers	Brain Angular Gyrus	brain
21	chr15:44217800-44218800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr15:44217800-44218800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:44217800-44219000	Enhancers	HMEC	breast
24	chr15:44217800-44219800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr15:44217800-44219800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr15:44217800-44220800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:44217800-44223200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr15:44217800-44223200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr15:44217800-44223200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:44218000-44218600	Enhancers	Brain Cingulate Gyrus	brain
31	chr15:44218000-44219600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:44218000-44219800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr15:44218000-44219800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:44218000-44219800	Enhancers	NHEK	skin
35	chr15:44218000-44220800	Enhancers	H1 Cell Line	embryonic stem cell
36	chr15:44218000-44220800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr15:44218000-44221800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:44218000-44223200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:44218000-44225600	Enhancers	Fetal Heart	heart
40	chr15:44218200-44219600	Enhancers	H9 Cell Line	embryonic stem cell
41	chr15:44218200-44222200	Weak transcription	NHDF-Ad	bronchial
42	chr15:44218200-44222200	Weak transcription	NHLF	lung
43	chr15:44218400-44218600	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr15:44218400-44219000	Enhancers	Brain Hippocampus Middle	brain
45	chr15:44218400-44219600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:44218400-44222200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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