Variant report

Variant	rs12779641
Chromosome Location	chr10:18821074-18821075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10508562	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10508563	0.94[CEU][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11014981	0.81[YRI][hapmap]
rs11015435	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap]
rs11511084	0.80[YRI][hapmap]
rs11540309	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs11597110	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11815228	1.00[CEU][hapmap]
rs12762481	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap]
rs12764334	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12764398	0.90[EUR][1000 genomes]
rs12765238	0.81[AFR][1000 genomes]
rs12766105	1.00[CEU][hapmap]
rs12766314	1.00[CEU][hapmap];0.85[LWK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs12767923	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs12768464	0.93[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap]
rs12769425	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs12770851	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs12772009	0.92[CEU][hapmap]
rs12772058	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12772522	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs12773254	0.82[EUR][1000 genomes]
rs12774593	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12778035	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs12781208	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs12784387	0.81[YRI][hapmap]
rs12784555	0.87[CEU][hapmap]
rs12784986	1.00[CEU][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap]
rs12785031	1.00[CEU][hapmap]
rs1880681	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2130531	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap]
rs2171922	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs2228645	1.00[CEU][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3740104	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs4237349	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs4310518	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs4314963	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4468242	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap]
rs4747355	0.81[AFR][1000 genomes]
rs4748487	0.81[AFR][1000 genomes]
rs4748490	0.82[AFR][1000 genomes]
rs4748496	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs4748499	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs56386348	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7072624	1.00[CEU][hapmap]
rs7072963	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs7096923	0.87[CEU][hapmap];0.90[TSI][hapmap]
rs7099423	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs7897159	1.00[CEU][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap]
rs7898513	0.82[TSI][hapmap]
rs7904016	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs7904949	0.86[CEU][hapmap];0.83[YRI][hapmap]
rs7905365	0.93[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs7923480	0.80[CEU][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	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1042073	chr10:18806900-18838303	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12779641	CACNB2	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18792400-18825400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr10:18799800-18825200	Weak transcription	Colonic Mucosa	Colon
3	chr10:18800200-18826800	Weak transcription	Brain Substantia Nigra	brain
4	chr10:18800400-18827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:18802000-18825000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:18802600-18828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:18802600-18828200	Weak transcription	Lung	lung
8	chr10:18807200-18826800	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:18807400-18828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:18808000-18828000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:18808400-18827000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr10:18808800-18825400	Weak transcription	Fetal Brain Female	brain
13	chr10:18809000-18824000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:18809000-18827000	Weak transcription	Small Intestine	intestine
15	chr10:18810400-18828000	Weak transcription	Brain Angular Gyrus	brain
16	chr10:18810600-18827000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:18810600-18828200	Weak transcription	Aorta	Aorta
18	chr10:18810800-18825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:18810800-18828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr10:18811000-18825400	Weak transcription	Right Ventricle	heart
21	chr10:18811000-18826800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:18812400-18825200	Weak transcription	Brain Anterior Caudate	brain
23	chr10:18812400-18827000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr10:18812600-18823000	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:18812800-18827000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:18814000-18828000	Weak transcription	Esophagus	oesophagus
27	chr10:18814600-18825200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:18814600-18827000	Weak transcription	Thymus	Thymus
29	chr10:18814800-18825200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr10:18814800-18825400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr10:18814800-18827600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr10:18815000-18826800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr10:18815200-18825400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:18815200-18843600	Weak transcription	A549	lung
35	chr10:18815800-18828000	Weak transcription	K562	blood
36	chr10:18816400-18830400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr10:18816400-18841800	Strong transcription	Liver	Liver
38	chr10:18816800-18829600	Weak transcription	HSMMtube	muscle
39	chr10:18817400-18821800	Weak transcription	Fetal Kidney	kidney
40	chr10:18817400-18829000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr10:18818000-18821800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr10:18818200-18824000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr10:18818200-18825800	Weak transcription	Psoas Muscle	Psoas
44	chr10:18818600-18824200	Weak transcription	Fetal Stomach	stomach
45	chr10:18818600-18825200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:18818600-18825200	Weak transcription	Pancreas	Pancrea
47	chr10:18818800-18828000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr10:18818800-18828400	Weak transcription	Fetal Thymus	thymus
49	chr10:18819000-18825400	Weak transcription	Brain Germinal Matrix	brain
50	chr10:18819200-18822200	Weak transcription	Rectal Mucosa Donor 29	rectum

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