Variant report

Variant	rs1427266
Chromosome Location	chr12:40708922-40708923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10459265	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10467144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10467146	0.86[CHB][hapmap]
rs10735931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735934	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10748029	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10748030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748031	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10748033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784486	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs10784501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784548	0.86[CHB][hapmap]
rs10878358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878368	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[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878377	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10878405	0.82[CHB][hapmap]
rs10878441	0.90[CHB][hapmap]
rs11176013	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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426362	0.86[CHB][hapmap]
rs1427263	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs1427264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427265	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[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427267	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs17444124	0.86[CHB][hapmap]
rs17466605	0.86[CHB][hapmap]
rs1896252	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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1896253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1896254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069228	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2114568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114569	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404581	0.81[CHB][hapmap]
rs2896975	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs3761863	0.86[CHB][hapmap]
rs3886747	0.81[CHB][hapmap]
rs4310676	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs4483664	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs4767969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767973	0.86[CHB][hapmap]
rs4768224	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs4768227	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768236	0.86[CHB][hapmap]
rs4768237	0.86[CHB][hapmap]
rs6581667	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6581668	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7137160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7137665	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs721709	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs721711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721713	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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298930	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[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302503	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7305344	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7307276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307562	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7308193	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs7488873	0.86[ASN][1000 genomes]
rs7957057	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.86[ASN][1000 genomes]
rs7973479	0.85[CHB][hapmap]
rs7979341	0.83[ASN][1000 genomes]
rs963243	0.86[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1042967	chr12:40629636-40710319	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1427266	CPNE8	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
2	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
3	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:40659600-40711200	Weak transcription	Aorta	Aorta
5	chr12:40673400-40713400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:40674400-40760400	Weak transcription	Lung	lung
7	chr12:40677000-40712200	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:40680400-40709000	Weak transcription	Ovary	ovary
9	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:40684000-40722600	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:40684000-40722600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:40684000-40725000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:40690400-40709200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:40692400-40711600	Weak transcription	Adipose Nuclei	Adipose
16	chr12:40695800-40723600	Weak transcription	Brain Angular Gyrus	brain
17	chr12:40699600-40721800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:40704400-40709000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:40704400-40723800	Weak transcription	Brain Anterior Caudate	brain
20	chr12:40704800-40709000	Weak transcription	Liver	Liver
21	chr12:40705600-40722400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:40706800-40709200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:40706800-40722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:40707000-40719000	Weak transcription	A549	lung
25	chr12:40707800-40724400	Strong transcription	Primary B cells from cord blood	blood
26	chr12:40708000-40709000	Enhancers	Primary B cells from peripheral blood	blood
27	chr12:40708200-40709800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:40708600-40709400	Enhancers	GM12878-XiMat	blood
29	chr12:40708800-40709800	Strong transcription	Left Ventricle	heart

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