Variant report

Variant	rs62190904
Chromosome Location	chr2:208893649-208893650
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr2:208893390-208893656	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:208613239..208615639-chr2:208892236..208894699,2	MCF-7	breast:
2	chr2:208888881..208890563-chr2:208892977..208895909,2	K562	blood:

Variant related genes	Relation type
PLEKHM3	TF binding region
ENSG00000163249	Chromatin interaction
ENSG00000178385	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10932224	0.82[EUR][1000 genomes]
rs12465292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12471242	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13431014	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1452521	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17459574	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17459758	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17537670	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17538061	0.81[EUR][1000 genomes]
rs2362787	0.83[EUR][1000 genomes]
rs28463196	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4502388	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62190863	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62190896	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62190898	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62190900	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62190905	1.00[AFR][1000 genomes];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	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6740362	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	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7588162	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs930745	0.91[AMR][1000 genomes];0.87[EUR][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	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
5	nsv961925	chr2:208892380-208897020	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208890800-208895400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:208890800-208896200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:208890800-208899400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:208891000-208894800	Weak transcription	Psoas Muscle	Psoas
5	chr2:208891000-208895400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:208891000-208895400	Weak transcription	Fetal Intestine Large	intestine
7	chr2:208891000-208895400	Weak transcription	Lung	lung
8	chr2:208891000-208896000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:208891000-208896000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:208891000-208896000	Weak transcription	Adipose Nuclei	Adipose
11	chr2:208891000-208896200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:208891000-208896200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:208891000-208896200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:208891000-208896200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:208891000-208896400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:208891000-208896400	Weak transcription	GM12878-XiMat	blood
17	chr2:208891000-208896400	Weak transcription	HMEC	breast
18	chr2:208891000-208904200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:208891000-208905400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:208891200-208895400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr2:208891200-208895600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:208891800-208894200	Weak transcription	HepG2	liver
23	chr2:208892200-208895200	Weak transcription	Placenta	Placenta

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