Variant report

Variant	rs11169258
Chromosome Location	chr12:39113040-39113041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10506124	0.87[ASN][1000 genomes]
rs10506125	0.80[MEX][hapmap];0.88[EUR][1000 genomes]
rs10506126	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10506127	0.82[CEU][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs10783317	0.86[JPT][hapmap]
rs10783329	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783330	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783333	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875953	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875954	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876005	0.87[EUR][1000 genomes]
rs10876008	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169006	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169054	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169087	0.88[JPT][hapmap]
rs11169100	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169189	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169222	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169482	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs11169518	0.88[CEU][hapmap]
rs11169519	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs11169535	0.87[CEU][hapmap]
rs11169807	1.00[ASW][hapmap]
rs12229104	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12231313	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12300353	0.84[AMR][1000 genomes]
rs12314639	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12424190	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12818797	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12822023	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12831609	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1352121	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1386018	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1400280	1.00[ASW][hapmap]
rs1403521	1.00[ASW][hapmap]
rs1523118	1.00[ASW][hapmap]
rs1564978	0.88[JPT][hapmap]
rs1586373	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs1875609	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2220267	0.86[JPT][hapmap]
rs34311455	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35254764	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3759139	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3803020	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap]
rs3887436	0.84[CEU][hapmap]
rs4616077	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61937754	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7309400	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7312879	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7315271	1.00[ASW][hapmap];0.80[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap]
rs7316392	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7960616	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971075	0.88[JPT][hapmap]
rs7979541	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9325144	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11169258	CPNE8	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
3	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
4	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:39079200-39114400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:39080600-39115600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:39083400-39113200	Weak transcription	Left Ventricle	heart
8	chr12:39086000-39114400	Weak transcription	Aorta	Aorta
9	chr12:39087200-39113800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:39089200-39113800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:39092600-39153600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:39094600-39114600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:39095000-39114000	Weak transcription	Liver	Liver
14	chr12:39095200-39114000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:39095800-39114600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:39095800-39117800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:39096800-39113800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:39109800-39116800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:39110400-39114600	Weak transcription	Adipose Nuclei	Adipose
20	chr12:39110800-39114200	Weak transcription	Right Ventricle	heart
21	chr12:39110800-39119800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:39111000-39114000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:39111000-39115600	Weak transcription	GM12878-XiMat	blood
24	chr12:39111200-39114000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:39111400-39114600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:39111400-39115200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:39111800-39114600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:39111800-39119400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:39112000-39114400	Weak transcription	Lung	lung
30	chr12:39112400-39115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:39112400-39118400	Weak transcription	Fetal Intestine Small	intestine
32	chr12:39112800-39114400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:39113000-39114600	Weak transcription	Esophagus	oesophagus
34	chr12:39113000-39114600	Weak transcription	Spleen	Spleen
35	chr12:39113000-39114800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:39113000-39117200	Weak transcription	Colonic Mucosa	Colon

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