Variant report

Variant	rs2466918
Chromosome Location	chr4:106265348-106265349
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:227664246..227665825-chr4:106265178..106268166,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169047	Chromatin interaction
ENSG00000272622	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2077608	0.80[CEU][hapmap]
rs2133086	0.88[CEU][hapmap]
rs2466917	0.93[ASN][1000 genomes]
rs2636732	0.80[CEU][hapmap]
rs2636734	0.83[CEU][hapmap]
rs2636741	0.84[CEU][hapmap]
rs2636742	0.83[CEU][hapmap]
rs2636743	0.80[CEU][hapmap]
rs2647237	0.98[ASN][1000 genomes]
rs2647238	0.85[EUR][1000 genomes]
rs2647250	0.83[CEU][hapmap]
rs2647258	0.93[ASN][1000 genomes]
rs2713831	0.80[CEU][hapmap]
rs2713834	0.80[CEU][hapmap]
rs2713860	0.84[CEU][hapmap]
rs2713863	0.84[CEU][hapmap]
rs2713873	0.80[CEU][hapmap]
rs2726455	0.80[CEU][hapmap]
rs2726475	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2726476	0.84[ASN][1000 genomes]
rs2726479	0.82[EUR][1000 genomes]
rs2726482	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2726485	0.96[ASN][1000 genomes]
rs2726526	0.80[CEU][hapmap]
rs36131630	0.82[ASN][1000 genomes]
rs7670522	0.82[CEU][hapmap]
rs7678440	0.82[CEU][hapmap]
rs7683416	0.82[CEU][hapmap]
rs7698080	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs923589	0.80[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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS 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 target site	41 gene(s)	inside rSNPs	diseases
6	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2466918	TET2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106234400-106266600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:106245600-106266400	Weak transcription	Gastric	stomach
3	chr4:106252000-106287400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:106253800-106266200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:106253800-106343000	Weak transcription	Psoas Muscle	Psoas
6	chr4:106254000-106274000	Weak transcription	Left Ventricle	heart
7	chr4:106254000-106280600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:106254200-106280600	Weak transcription	Aorta	Aorta
9	chr4:106256200-106280200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:106264400-106265400	Enhancers	Fetal Kidney	kidney
11	chr4:106264400-106265400	Enhancers	Fetal Stomach	stomach
12	chr4:106264600-106265400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:106264800-106267400	Enhancers	HepG2	liver
14	chr4:106265000-106265400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:106265000-106265800	Weak transcription	Ovary	ovary
16	chr4:106265000-106266400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:106265000-106280600	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:106265200-106265400	Enhancers	Adipose Nuclei	Adipose
19	chr4:106265200-106265600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:106265200-106265600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:106265200-106266200	Enhancers	Fetal Lung	lung

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