Variant report

Variant	rs296742
Chromosome Location	chr12:50335086-50335087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1077520	0.81[CEU][hapmap]
rs2878771	0.80[CEU][hapmap]
rs3741559	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs416959	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv899072	chr12:50326176-50379667	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs296742	DDX23	cis	cerebellum	SCAN
rs296742	ADCY6	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50323400-50338800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:50327200-50338600	Weak transcription	Fetal Thymus	thymus
3	chr12:50328800-50335800	Weak transcription	Hela-S3	cervix
4	chr12:50331000-50338800	Weak transcription	Fetal Brain Female	brain
5	chr12:50332400-50336800	Weak transcription	Gastric	stomach
6	chr12:50332600-50336200	Weak transcription	NHEK	skin
7	chr12:50332600-50336800	Weak transcription	HMEC	breast
8	chr12:50332800-50336800	Weak transcription	Pancreas	Pancrea
9	chr12:50333400-50336400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:50333800-50335400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:50333800-50336400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:50333800-50336400	Weak transcription	Fetal Lung	lung
13	chr12:50333800-50338600	Weak transcription	Right Atrium	heart
14	chr12:50334000-50335800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:50334000-50336200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:50334000-50336800	Weak transcription	Stomach Mucosa	stomach
17	chr12:50334000-50339200	Weak transcription	Lung	lung
18	chr12:50334800-50335800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:50334800-50335800	Weak transcription	Esophagus	oesophagus

Quick Search:

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

what's new

Quick links