Variant report

Variant	rs12621474
Chromosome Location	chr2:53631110-53631111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10165455	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10176195	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10193852	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10205628	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1157474	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12466120	0.86[EUR][1000 genomes]
rs12473169	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13398039	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13415193	0.89[AMR][1000 genomes]
rs13422294	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2161781	0.84[AFR][1000 genomes]
rs28497726	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28879825	0.89[AMR][1000 genomes]
rs55776553	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62139894	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72893556	0.81[AFR][1000 genomes]
rs72905033	0.81[AFR][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	nsv1002145	chr2:53387912-53832213	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv535718	chr2:53387912-53832213	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv874143	chr2:53499062-53643093	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv997401	chr2:53515629-53863347	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3383918	chr2:53585059-53710179	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53628200-53635800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:53628200-53635800	Enhancers	HMEC	breast
3	chr2:53629200-53632000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:53629200-53632400	Enhancers	NHEK	skin
5	chr2:53629800-53632600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:53630200-53632600	Enhancers	Hela-S3	cervix
7	chr2:53630400-53631800	Enhancers	Osteobl	bone
8	chr2:53630600-53631400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:53630800-53631400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:53630800-53631400	Enhancers	NH-A	brain
11	chr2:53631000-53631400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr2:53631000-53631600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:53631000-53631600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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