Variant report

Variant	rs12423250
Chromosome Location	chr12:48389245-48389246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48346353..48348105-chr12:48388384..48390746,2	MCF-7	breast:
2	chr12:48375884..48381022-chr12:48386743..48391938,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1049392	0.94[JPT][hapmap]
rs10747529	0.94[JPT][hapmap]
rs10875733	0.94[JPT][hapmap]
rs10875739	0.94[JPT][hapmap]
rs10875752	0.94[JPT][hapmap]
rs10875754	0.94[JPT][hapmap]
rs10875761	0.94[JPT][hapmap]
rs11168350	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11168353	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap]
rs11168354	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11168358	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs11168363	0.94[JPT][hapmap]
rs11168364	0.94[JPT][hapmap]
rs11168373	0.93[JPT][hapmap]
rs11168404	0.94[JPT][hapmap]
rs11168417	0.94[JPT][hapmap]
rs11168424	0.94[JPT][hapmap]
rs11168434	0.94[JPT][hapmap]
rs11168435	0.94[JPT][hapmap]
rs11168438	0.91[JPT][hapmap]
rs11168445	0.93[JPT][hapmap]
rs11168448	0.94[JPT][hapmap]
rs12422355	0.94[JPT][hapmap]
rs17122567	0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs1793958	0.83[JPT][hapmap]
rs1793960	0.87[CEU][hapmap];0.89[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2286020	0.94[JPT][hapmap]
rs2408954	0.94[JPT][hapmap]
rs3742075	0.86[JPT][hapmap]
rs3825403	0.94[JPT][hapmap]
rs4258439	0.94[JPT][hapmap]
rs7299704	0.94[JPT][hapmap]
rs7302354	0.94[JPT][hapmap]
rs7303677	0.94[JPT][hapmap]
rs7484942	0.94[JPT][hapmap]
rs765260	0.94[JPT][hapmap]
rs7962390	0.94[JPT][hapmap]
rs7962569	0.87[JPT][hapmap]
rs8181670	0.94[JPT][hapmap]
rs886589	0.94[JPT][hapmap]
rs954326	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs9651981	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9669263	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9804751	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]

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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12423250	CCNT1	cis	parietal	SCAN
rs12423250	C12orf41	cis	parietal	SCAN
rs12423250	TMEM106C	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48385200-48391600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:48385600-48389600	Weak transcription	Right Atrium	heart
7	chr12:48385800-48389600	Weak transcription	Left Ventricle	heart
8	chr12:48385800-48389600	Weak transcription	Lung	lung
9	chr12:48386000-48389600	Weak transcription	Right Ventricle	heart
10	chr12:48386400-48389800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:48386800-48392800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:48387000-48391600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:48387600-48390200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:48388000-48391400	Enhancers	Fetal Brain Male	brain
15	chr12:48388600-48389400	Bivalent Enhancer	Fetal Lung	lung
16	chr12:48388600-48389400	Weak transcription	Psoas Muscle	Psoas
17	chr12:48388600-48390400	Enhancers	Brain Germinal Matrix	brain
18	chr12:48388800-48389400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:48388800-48390200	Strong transcription	Fetal Intestine Small	intestine
20	chr12:48389000-48390600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:48389000-48390600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr12:48389200-48390400	Bivalent Enhancer	Fetal Stomach	stomach
23	chr12:48389200-48390400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr12:48389200-48391000	Enhancers	Cortex derived primary cultured neurospheres	brain

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