Variant report

Variant	rs1398946
Chromosome Location	chr4:90055899-90055900
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	chr4:90043352..90045261-chr4:90054968..90057885,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10007590	1.00[JPT][hapmap]
rs10020832	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17817631	1.00[JPT][hapmap]
rs2446306	0.82[JPT][hapmap]
rs5029557	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6842150	0.81[ASN][1000 genomes]
rs7687207	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv470052	chr4:90055898-90075384	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90044800-90056000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:90046000-90056200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:90050800-90059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:90051000-90056000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:90051200-90056000	Weak transcription	NHLF	lung
6	chr4:90051400-90056000	Weak transcription	Osteobl	bone
7	chr4:90052400-90056000	Weak transcription	A549	lung
8	chr4:90052800-90056000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:90054800-90056000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:90055200-90056000	Weak transcription	NH-A	brain
11	chr4:90055200-90056200	Enhancers	NHDF-Ad	bronchial
12	chr4:90055400-90056400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:90055400-90057000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:90055400-90058200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:90055800-90056000	Active TSS	Brain Anterior Caudate	brain
16	chr4:90055800-90056000	Enhancers	Brain Cingulate Gyrus	brain
17	chr4:90055800-90056000	Enhancers	Brain Hippocampus Middle	brain
18	chr4:90055800-90056200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:90055800-90056200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr4:90055800-90056200	Enhancers	Fetal Intestine Large	intestine
21	chr4:90055800-90056600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:90055800-90058600	Enhancers	NHEK	skin

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