Variant report

Variant	rs11612004
Chromosome Location	chr12:39204282-39204283
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10506129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10875979	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10875991	0.83[AMR][1000 genomes]
rs10876086	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876149	1.00[ASW][hapmap];0.95[MEX][hapmap];0.84[AFR][1000 genomes]
rs10876163	0.84[AFR][1000 genomes]
rs1095575	0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs11169031	0.81[AMR][1000 genomes]
rs11169169	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs11169301	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11169387	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169511	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169547	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169769	0.84[AFR][1000 genomes]
rs11169801	0.84[AFR][1000 genomes]
rs11169879	0.84[AFR][1000 genomes]
rs11169908	0.84[ASW][hapmap]
rs11514111	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11523606	0.84[AMR][1000 genomes]
rs11523607	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11609849	0.84[AFR][1000 genomes]
rs11610376	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11613205	0.84[AFR][1000 genomes]
rs11615668	0.84[AFR][1000 genomes]
rs12812262	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1352122	0.96[CEU][hapmap]
rs1352123	0.96[CEU][hapmap]
rs1403523	0.96[CEU][hapmap]
rs1486345	0.96[CEU][hapmap]
rs1486357	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs1554550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1601579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1684395	0.85[CEU][hapmap]
rs1684415	0.96[CEU][hapmap]
rs1684416	0.91[CEU][hapmap]
rs1719848	0.85[CEU][hapmap]
rs1719852	0.96[CEU][hapmap]
rs1719855	0.96[CEU][hapmap]
rs1719858	0.95[CEU][hapmap]
rs17464772	0.84[AFR][1000 genomes]
rs17465893	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17523988	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1843639	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2069211	0.96[CEU][hapmap];0.90[GIH][hapmap]
rs2388060	0.84[ASW][hapmap]
rs36035670	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3886109	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55828987	0.81[AMR][1000 genomes]
rs6580755	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7301104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7960621	0.84[AFR][1000 genomes]
rs7973992	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs826838	0.89[CEU][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap]
rs826851	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs826858	0.96[CEU][hapmap]
rs826870	0.96[CEU][hapmap];0.90[GIH][hapmap]
rs826876	0.96[CEU][hapmap]
rs826879	0.92[CEU][hapmap]
rs826886	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs864324	0.85[CEU][hapmap]
rs980571	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap]
rs980572	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[TSI][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	nsv676	chr12:39184359-39215822	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
2	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11612004	CPNE8	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39184200-39205800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:39200800-39205000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:39201200-39208000	Weak transcription	A549	lung
4	chr12:39201600-39208800	Weak transcription	Esophagus	oesophagus
5	chr12:39201800-39205600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:39201800-39216600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:39202800-39204800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:39203200-39213400	Weak transcription	Pancreas	Pancrea
9	chr12:39203200-39220200	Weak transcription	Psoas Muscle	Psoas
10	chr12:39203200-39276000	Weak transcription	Aorta	Aorta
11	chr12:39203400-39204600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:39203400-39204600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:39203400-39205800	Weak transcription	Liver	Liver
14	chr12:39203600-39216800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:39203800-39205800	Weak transcription	Ovary	ovary
16	chr12:39204000-39204600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:39204000-39205200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:39204000-39205600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:39204000-39205600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:39204000-39205600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:39204000-39206000	Strong transcription	Primary hematopoietic stem cells	blood
22	chr12:39204000-39284800	Weak transcription	Lung	lung
23	chr12:39204200-39205800	Weak transcription	Left Ventricle	heart
24	chr12:39204200-39213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:39204200-39216800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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