Variant report

Variant	rs28928309
Chromosome Location	chr2:113834739-113834740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113834467..113836706-chr2:113841489..113843964,2	MCF-7	breast:
2	chr2:113825741..113828601-chr2:113834628..113836423,2	MCF-7	breast:
3	chr2:113827867..113831764-chr2:113833015..113836168,5	MCF-7	breast:
4	chr2:113718593..113720289-chr2:113834611..113837557,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136697	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12475887	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13032281	0.91[ASN][1000 genomes]
rs1618084	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1665189	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1688075	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1688076	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1794071	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867829	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs315925	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315929	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs315932	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3811058	0.91[EUR][1000 genomes]
rs4848314	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4849151	0.80[EUR][1000 genomes]
rs4989179	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55932259	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56011414	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57130564	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62158848	0.94[ASN][1000 genomes]
rs66613854	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66615594	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv2881	chr2:113800805-113846597	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113825800-113839600	Enhancers	HMEC	breast
2	chr2:113832400-113835600	Enhancers	Fetal Intestine Small	intestine
3	chr2:113832600-113835000	Enhancers	Fetal Intestine Large	intestine
4	chr2:113832600-113835800	Weak transcription	Lung	lung
5	chr2:113832800-113835800	Weak transcription	Esophagus	oesophagus
6	chr2:113834000-113835600	Enhancers	NHEK	skin
7	chr2:113834000-113838200	Enhancers	Stomach Mucosa	stomach
8	chr2:113834200-113835000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr2:113834600-113835000	Enhancers	Gastric	stomach
10	chr2:113834600-113835000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr2:113834600-113836000	Enhancers	Fetal Muscle Trunk	muscle
12	chr2:113834600-113836800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:113834600-113837400	Enhancers	Fetal Muscle Leg	muscle
14	chr2:113834600-113837800	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:113834600-113838200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:113834600-113840000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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