Variant report

Variant	rs2723264
Chromosome Location	chr12:40652520-40652521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10506155	1.00[CHB][hapmap]
rs10784451	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784452	0.85[ASN][1000 genomes]
rs10784532	1.00[CHB][hapmap]
rs10878258	0.87[CHB][hapmap]
rs10878278	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878284	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878343	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10878356	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10878372	1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs11175729	0.80[ASN][1000 genomes]
rs11175843	1.00[CHB][hapmap];0.85[JPT][hapmap];0.99[ASN][1000 genomes]
rs11175934	0.97[ASN][1000 genomes]
rs11175935	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs11175958	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11175966	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11176118	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11176153	1.00[CHB][hapmap]
rs11176418	0.93[CHB][hapmap]
rs12368229	1.00[CHB][hapmap];0.80[GIH][hapmap]
rs17444223	1.00[CHB][hapmap]
rs17444730	0.93[CHB][hapmap]
rs17462055	1.00[CHB][hapmap]
rs2162471	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7132187	1.00[CHB][hapmap]
rs7134379	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs7137173	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs715403	0.92[CHB][hapmap]
rs7303525	1.00[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap]
rs7311850	1.00[CHB][hapmap]
rs7966550	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[ASN][1000 genomes]
rs7969677	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[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	nsv1045408	chr12:40620554-40664424	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2723264	C12orf40	cis	temporal cortex	BrainEAC

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
3	chr12:40619800-40658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:40620800-40659200	Weak transcription	Brain Anterior Caudate	brain
5	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
6	chr12:40621000-40659800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:40621000-40661200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:40622800-40661000	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
10	chr12:40630600-40669400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:40630600-40686400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:40632000-40655200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:40632000-40656000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr12:40633400-40654200	Weak transcription	Aorta	Aorta
15	chr12:40640200-40680400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
17	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
18	chr12:40641200-40662800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:40642200-40682400	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:40643000-40659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:40643400-40655200	Strong transcription	Primary B cells from cord blood	blood
22	chr12:40646800-40658000	Weak transcription	A549	lung
23	chr12:40647000-40653000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:40647600-40674000	Weak transcription	Lung	lung
25	chr12:40648400-40653800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:40648600-40657600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:40648800-40659200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:40648800-40659800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:40649000-40659200	Weak transcription	Ovary	ovary
30	chr12:40649400-40653000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:40649600-40657800	Weak transcription	Adipose Nuclei	Adipose
32	chr12:40649600-40659200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:40650400-40656000	Strong transcription	Liver	Liver
34	chr12:40652000-40652600	Weak transcription	Primary B cells from peripheral blood	blood

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