Variant report

Variant	rs2370414
Chromosome Location	chr12:2368396-2368397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1006737	0.82[MEX][hapmap]
rs1860002	0.82[CEU][hapmap];0.84[CHB][hapmap]
rs2007044	0.92[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs2159100	0.82[MEX][hapmap]
rs2238057	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239038	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[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];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2370413	0.81[CHB][hapmap];0.81[TSI][hapmap]
rs34382810	0.83[EUR][1000 genomes]
rs4765905	0.82[MEX][hapmap]
rs4765911	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7297582	0.81[CEU][hapmap]
rs758170	0.82[MEX][hapmap]
rs882194	0.85[CEU][hapmap];0.81[CHD][hapmap];0.81[EUR][1000 genomes]
rs882195	0.81[CHD][hapmap];0.84[JPT][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	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2370414	CACNA1C	cis	cerebellum	SCAN
rs2370414	AKAP3	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2361400-2370600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:2365000-2369200	Enhancers	Osteobl	bone
3	chr12:2365200-2368400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:2365200-2368400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:2365200-2368400	Weak transcription	Fetal Stomach	stomach
6	chr12:2365200-2369000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:2365200-2369000	Weak transcription	Aorta	Aorta
8	chr12:2365200-2369000	Weak transcription	Lung	lung
9	chr12:2365200-2369000	Weak transcription	Right Atrium	heart
10	chr12:2365200-2369200	Weak transcription	Fetal Intestine Large	intestine
11	chr12:2365200-2371400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:2365200-2372800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:2365200-2373000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:2365200-2373400	Weak transcription	Adipose Nuclei	Adipose
15	chr12:2365200-2373600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:2365200-2374200	Weak transcription	Brain Anterior Caudate	brain
17	chr12:2365400-2368400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:2365400-2368400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:2365400-2368400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:2365400-2368400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:2365400-2368600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:2365400-2369000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:2365400-2369000	Weak transcription	Spleen	Spleen
24	chr12:2365400-2369200	Weak transcription	Fetal Intestine Small	intestine
25	chr12:2365400-2373200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:2365400-2374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:2365400-2374400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:2365400-2374800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:2365400-2376000	Weak transcription	Brain Angular Gyrus	brain
30	chr12:2366000-2373200	Weak transcription	HSMMtube	muscle
31	chr12:2366200-2369400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr12:2366400-2371000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:2366400-2373200	Weak transcription	NH-A	brain
34	chr12:2366800-2368800	Enhancers	Fetal Heart	heart
35	chr12:2366800-2370000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:2367000-2368400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:2367000-2368400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr12:2367000-2370000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr12:2367200-2368400	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:2367200-2368600	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:2367200-2369200	Enhancers	NHDF-Ad	bronchial
42	chr12:2367200-2369600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr12:2367200-2370000	Enhancers	Primary hematopoietic stem cells	blood
44	chr12:2367400-2370800	Weak transcription	NHLF	lung
45	chr12:2367600-2369400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:2367600-2369400	Enhancers	Primary T cells from cord blood	blood
47	chr12:2367800-2369600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:2368000-2368800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:2368000-2369200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:2368000-2369400	Enhancers	Fetal Thymus	thymus

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