Variant report

Variant	rs12123538
Chromosome Location	chr1:184353248-184353249
allele	A/C
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	HDAC2	chr1:184352915-184353319	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr1:184352922-184353491	H1-hESC	embryonic stem cell:	n/a	chr1:184352997-184353009 chr1:184353149-184353158 chr1:184352999-184353008
3	EP300	chr1:184352916-184353281	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:184349850..184351916-chr1:184352544..184355292,2	K562	blood:
2	chr1:184353036..184355475-chr1:184360672..184362232,2	MCF-7	breast:
3	chr1:184347794..184350297-chr1:184351548..184353524,2	MCF-7	breast:

Variant related genes	Relation type
C1orf21	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10911585	0.95[EUR][1000 genomes]
rs10911586	0.95[EUR][1000 genomes]
rs10911597	0.81[EUR][1000 genomes]
rs11799574	1.00[CEU][hapmap]
rs12116705	0.97[EUR][1000 genomes]
rs12128343	1.00[CEU][hapmap]
rs12128424	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12129504	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12130008	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12131730	0.92[EUR][1000 genomes]
rs12132220	0.88[EUR][1000 genomes]
rs12136470	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12140904	0.95[EUR][1000 genomes]
rs12142338	0.81[EUR][1000 genomes]
rs12142568	1.00[CEU][hapmap]
rs12142676	0.81[EUR][1000 genomes]
rs12145326	1.00[CEU][hapmap]
rs12354368	0.97[EUR][1000 genomes]
rs13374592	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16823133	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17576899	0.97[EUR][1000 genomes]
rs17577247	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs56173711	0.95[EUR][1000 genomes]
rs60650088	0.95[EUR][1000 genomes]
rs6699949	0.84[EUR][1000 genomes]
rs74131663	0.84[EUR][1000 genomes]
rs74131672	0.81[EUR][1000 genomes]
rs74131673	0.81[EUR][1000 genomes]
rs9803754	0.90[EUR][1000 genomes]
rs9804057	0.90[EUR][1000 genomes]
rs9970469	1.00[CEU][hapmap];0.97[EUR][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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv3821	chr1:184319543-184365236	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr1:184337400-184355000	Weak transcription	Psoas Muscle	Psoas
2	chr1:184346000-184355000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:184346200-184355000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:184348400-184355000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:184348800-184355000	Weak transcription	Fetal Heart	heart
6	chr1:184348800-184355000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:184349000-184355000	Weak transcription	NHLF	lung
8	chr1:184350400-184355000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:184350400-184355000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:184350600-184354600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:184350600-184355000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:184351800-184353800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr1:184351800-184354000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:184351800-184354600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:184351800-184354800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:184352000-184354400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:184352200-184354400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:184352200-184355000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:184352600-184353800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:184352800-184353400	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:184352800-184353400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:184353000-184353600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:184353200-184354200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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