Variant report

Variant	rs12939122
Chromosome Location	chr17:38857190-38857191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38775996..38776776-chr17:38857123..38857985,2	MCF-7	breast:
2	chr17:38732045..38733357-chr17:38856954..38857905,11	MCF-7	breast:
3	chr17:38843380..38844345-chr17:38857058..38857983,7	MCF-7	breast:
4	chr17:38478633..38479142-chr17:38857062..38857578,2	MCF-7	breast:
5	chr17:38711497..38712257-chr17:38857125..38857877,3	MCF-7	breast:
6	chr17:38604655..38605626-chr17:38857061..38857980,4	MCF-7	breast:
7	chr17:38796377..38799257-chr17:38854775..38858682,3	MCF-7	breast:
8	chr17:38843380..38844410-chr17:38857012..38857999,19	MCF-7	breast:
9	chr17:38843400..38844347-chr17:38857080..38858005,7	MCF-7	breast:
10	chr17:38738290..38739117-chr17:38857024..38857827,3	MCF-7	breast:
11	chr17:38732045..38733142-chr17:38856954..38857905,8	MCF-7	breast:
12	chr17:38731979..38732799-chr17:38857038..38857899,2	MCF-7	breast:
13	chr17:38775973..38776776-chr17:38856990..38857985,3	MCF-7	breast:
14	chr17:38738608..38739117-chr17:38857059..38857827,2	MCF-7	breast:
15	chr17:38842259..38842805-chr17:38856975..38857595,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12938105	0.90[AFR][1000 genomes]
rs12945365	0.90[AFR][1000 genomes]
rs12945784	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12946793	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs35078263	0.90[AFR][1000 genomes]
rs35163875	1.00[AFR][1000 genomes]
rs35401703	0.90[AFR][1000 genomes]
rs35494992	0.90[AFR][1000 genomes]
rs35650621	0.90[AFR][1000 genomes]
rs35671506	1.00[AFR][1000 genomes]
rs35907708	0.90[AFR][1000 genomes]
rs36105662	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs60488918	0.90[AFR][1000 genomes]
rs71371441	1.00[AFR][1000 genomes]
rs71371442	0.90[AFR][1000 genomes]
rs71383382	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38853000-38859800	Weak transcription	Pancreas	Pancrea
2	chr17:38853200-38858400	Enhancers	Placenta Amnion	Placenta Amnion
3	chr17:38853400-38864000	Weak transcription	A549	lung
4	chr17:38853800-38859800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:38853800-38859800	Weak transcription	NHEK	skin
6	chr17:38853800-38864000	Weak transcription	Right Atrium	heart
7	chr17:38854000-38858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:38854000-38858600	Weak transcription	Hela-S3	cervix
9	chr17:38854000-38861800	Weak transcription	HMEC	breast
10	chr17:38854000-38875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:38856600-38861600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:38856800-38863600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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Input of quick search could be:

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

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