Variant report

Variant	rs924079
Chromosome Location	chr12:117253979-117253980
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117239479..117242263-chr12:117253396..117256340,3	K562	blood:
2	chr12:117172640..117175052-chr12:117251934..117254803,2	MCF-7	breast:
3	chr12:117248703..117251842-chr12:117252978..117255376,3	MCF-7	breast:
4	chr12:117251777..117254967-chr12:117255465..117258181,5	MCF-7	breast:
5	chr12:117243731..117245793-chr12:117253292..117254945,2	MCF-7	breast:
6	chr12:117253820..117255367-chr12:117255716..117257267,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10774888	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10850718	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10850719	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850721	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850724	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12301988	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12815898	0.89[EUR][1000 genomes]
rs1603327	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767457	0.95[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7313014	0.87[EUR][1000 genomes]
rs7314211	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7314377	0.89[CEU][hapmap]
rs7969141	0.90[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs924079	C12orf49	cis	parietal	SCAN
rs924079	MAPKAPK5	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117198000-117256200	Weak transcription	Hela-S3	cervix
2	chr12:117225200-117256200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:117228400-117256400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:117229200-117256200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:117237000-117256200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:117237200-117256200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:117237200-117256200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:117237800-117256000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:117237800-117256200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:117238000-117256200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:117238000-117256200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:117238400-117255600	Enhancers	Fetal Thymus	thymus
13	chr12:117242000-117256200	Weak transcription	GM12878-XiMat	blood
14	chr12:117242200-117256000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:117247000-117255800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:117247000-117256200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:117247200-117256000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:117248200-117256200	Weak transcription	Brain Germinal Matrix	brain
19	chr12:117249000-117256200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:117249400-117256200	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:117251200-117256000	Weak transcription	HepG2	liver
22	chr12:117251200-117256200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:117251400-117256200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:117251600-117254600	Enhancers	Thymus	Thymus
25	chr12:117251800-117255800	Enhancers	Primary B cells from cord blood	blood
26	chr12:117251800-117256000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:117252400-117254000	Weak transcription	Spleen	Spleen
28	chr12:117252800-117256200	Weak transcription	Placenta	Placenta

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