Variant report

Variant	rs428459
Chromosome Location	chr7:107818851-107818852
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	chr7:107818696..107821681-chr7:107992805..107995213,2	MCF-7	breast:
2	chr7:107817682..107823715-chr7:108094168..108099407,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs107588	0.82[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs107589	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs11761503	0.93[ASN][1000 genomes]
rs11974528	0.89[JPT][hapmap]
rs16872418	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2142325	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs371613	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs376375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819740	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs393266	0.89[JPT][hapmap]
rs394921	1.00[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs399543	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs401433	0.89[JPT][hapmap]
rs417455	0.89[JPT][hapmap]
rs420889	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs422327	0.82[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs427909	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs439652	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs441534	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs4730294	0.89[JPT][hapmap]
rs6962066	0.82[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs6970656	0.82[GIH][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv831089	chr7:107687618-107877240	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv888941	chr7:107796150-107863395	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1030222	chr7:107809927-107844916	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs428459	LAMB4	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107786800-107819000	Weak transcription	Brain Angular Gyrus	brain
2	chr7:107786800-107857800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:107787800-107844200	Weak transcription	Brain Germinal Matrix	brain
4	chr7:107791000-107824600	Weak transcription	HUVEC	blood vessel
5	chr7:107808200-107820000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:107811200-107820000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:107811800-107821400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:107813200-107819000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:107813600-107820000	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:107813800-107820000	Weak transcription	Fetal Brain Female	brain
11	chr7:107814200-107828400	Weak transcription	Fetal Intestine Small	intestine
12	chr7:107814800-107830400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:107815600-107829600	Weak transcription	Brain Substantia Nigra	brain
14	chr7:107816800-107821600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:107817000-107819000	Weak transcription	A549	lung
16	chr7:107817200-107819000	Weak transcription	Placenta	Placenta
17	chr7:107817400-107821800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:107817400-107828600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:107818200-107820800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:107818200-107851800	Weak transcription	HSMMtube	muscle
21	chr7:107818400-107820000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:107818400-107820000	Weak transcription	Fetal Intestine Large	intestine
23	chr7:107818400-107821600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:107818600-107819400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:107818600-107821000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr7:107818600-107848400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr7:107818800-107819200	Enhancers	Fetal Muscle Trunk	muscle
28	chr7:107818800-107819800	Strong transcription	Brain Anterior Caudate	brain
29	chr7:107818800-107820200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr7:107818800-107820800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:107818800-107820800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:107818800-107820800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:107818800-107821400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:107818800-107826400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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