Variant report

Variant	rs12072428
Chromosome Location	chr1:57574991-57574992
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11206974	1.00[EUR][1000 genomes]
rs11799770	1.00[EUR][1000 genomes]
rs11807035	1.00[EUR][1000 genomes]
rs11808294	1.00[EUR][1000 genomes]
rs11808305	1.00[EUR][1000 genomes]
rs13374012	1.00[EUR][1000 genomes]
rs35124225	1.00[EUR][1000 genomes]
rs59285318	1.00[EUR][1000 genomes]
rs6677976	1.00[EUR][1000 genomes]
rs6684103	1.00[EUR][1000 genomes]
rs6684287	1.00[EUR][1000 genomes]
rs6688025	1.00[EUR][1000 genomes]
rs6697460	1.00[EUR][1000 genomes]
rs706352	1.00[EUR][1000 genomes]
rs74074905	1.00[EUR][1000 genomes]
rs7529992	1.00[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers 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	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12072428	SATB1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57567400-57576800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:57571600-57575600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:57571600-57577600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:57571800-57575600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:57571800-57577000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:57572000-57576800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:57572200-57576800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:57572200-57577000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:57573400-57577400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:57573800-57575000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:57574200-57575000	Enhancers	Right Atrium	heart
13	chr1:57574200-57578000	Enhancers	Fetal Heart	heart
14	chr1:57574400-57575000	Enhancers	Left Ventricle	heart
15	chr1:57574400-57575000	Enhancers	Psoas Muscle	Psoas
16	chr1:57574400-57577600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:57574800-57575000	Enhancers	Placenta	Placenta
18	chr1:57574800-57575200	Enhancers	Liver	Liver

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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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