Variant report

Variant	rs12746741
Chromosome Location	chr1:84539576-84539577
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	chr1:84528524..84531344-chr1:84538975..84541375,2	MCF-7	breast:
2	chr1:84539350..84542065-chr1:84568304..84570726,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10493750	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11163897	0.83[JPT][hapmap]
rs11163898	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11163900	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11163905	0.86[GIH][hapmap]
rs11163906	0.86[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap]
rs11163907	0.86[GIH][hapmap]
rs12070547	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12119275	0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs12132032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12404263	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12405120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12724598	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12748859	0.82[MEX][hapmap]
rs1402694	0.86[GIH][hapmap]
rs1521518	0.85[GIH][hapmap];0.82[MEX][hapmap]
rs1565823	0.82[MEX][hapmap]
rs1874070	0.81[GIH][hapmap]
rs2134648	0.82[MEX][hapmap]
rs34179759	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34495740	0.89[ASN][1000 genomes]
rs35452337	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3861699	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3903924	0.83[ASN][1000 genomes]
rs3915908	0.83[ASN][1000 genomes]
rs6576962	0.86[GIH][hapmap]
rs6669045	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6674038	0.83[JPT][hapmap]
rs6703653	0.82[JPT][hapmap]
rs67276144	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72711192	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515976	0.82[MEX][hapmap]
rs7520283	0.82[JPT][hapmap]
rs953197	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs957828	0.83[JPT][hapmap]

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	nsv1732	chr1:84499098-84544635	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv871655	chr1:84517261-84550849	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3379138	chr1:84531980-84545128	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12746741	PRKACB	cis	lymphoblastoid	seeQTL
rs12746741	MCOLN2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84536600-84542400	Weak transcription	Fetal Lung	lung
2	chr1:84537600-84541000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:84537600-84541000	Weak transcription	K562	blood
4	chr1:84538000-84541200	Weak transcription	Liver	Liver
5	chr1:84538000-84542000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:84538400-84542400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:84538400-84542800	Weak transcription	HSMM	muscle
8	chr1:84538600-84542000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:84538600-84542400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:84538600-84542400	Weak transcription	Osteobl	bone
11	chr1:84538800-84542200	Weak transcription	Fetal Brain Male	brain
12	chr1:84539200-84542000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:84539200-84542400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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