Variant report

Variant	rs12465292
Chromosome Location	chr2:208897298-208897299
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10497895	0.86[CEU][hapmap]
rs10932224	0.82[EUR][1000 genomes]
rs12464255	0.86[CEU][hapmap]
rs12465052	0.86[CEU][hapmap]
rs12471242	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13431014	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1452521	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17459574	0.93[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17459758	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17537670	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17538061	0.86[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2362787	0.83[EUR][1000 genomes]
rs28463196	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4502388	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62190863	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62190896	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62190898	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62190900	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62190904	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62190905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62192772	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62192773	0.89[EUR][1000 genomes]
rs6435402	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6740362	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72969822	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72981543	0.85[EUR][1000 genomes]
rs7565251	0.84[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7588162	0.93[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs930745	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208890800-208899400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:208891000-208904200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:208891000-208905400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:208895200-208899200	Enhancers	Placenta	Placenta
5	chr2:208895400-208897600	Enhancers	Fetal Intestine Small	intestine
6	chr2:208895400-208897800	Enhancers	Fetal Intestine Large	intestine
7	chr2:208895600-208897400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:208895800-208897400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr2:208896000-208897400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:208896000-208897400	Enhancers	Adipose Nuclei	Adipose
11	chr2:208896400-208897400	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr2:208896600-208898400	Enhancers	HepG2	liver
13	chr2:208896600-208901000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:208896600-208907600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:208896800-208898000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:208896800-208898600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:208896800-208898600	Weak transcription	HMEC	breast
18	chr2:208897200-208898400	Weak transcription	GM12878-XiMat	blood

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