Variant report

Variant	rs2239038
Chromosome Location	chr12:2374130-2374131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:2373818-2374531	IMR90	lung:	n/a	chr12:2374249-2374260 chr12:2374248-2374261
2	TEAD4	chr12:2373861-2374708	SK-N-SH	brain:	n/a	n/a
3	EP300	chr12:2373720-2375060	SK-N-SH	brain:	n/a	chr12:2374062-2374072
4	TAF1	chr12:2374036-2374393	SK-N-SH	brain:	n/a	n/a
5	FOSL2	chr12:2373992-2374477	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr12:2373390-2375080	SK-N-SH	brain:	n/a	chr12:2373828-2373837
7	RAD21	chr12:2373988-2374800	IMR90	lung:	n/a	n/a
8	NFIC	chr12:2373409-2375048	SK-N-SH	brain:	n/a	chr12:2374645-2374662 chr12:2374645-2374661
9	MAX	chr12:2373930-2374628	SK-N-SH	brain:	n/a	n/a
10	MAX	chr12:2374014-2374708	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr12:2372316-2375602	U87	brain:	n/a	n/a
12	EP300	chr12:2373828-2374982	SK-N-SH	brain:	n/a	chr12:2374062-2374072
13	POLR2A	chr12:2372699-2375155	U87	brain:	n/a	n/a
14	REST	chr12:2374002-2374540	SK-N-SH	brain:	n/a	n/a
15	JUND	chr12:2373929-2374928	SK-N-SH	brain:	n/a	n/a
16	EP300	chr12:2373899-2376453	SK-N-SH	brain:	n/a	chr12:2374062-2374072
17	TCF12	chr12:2373290-2375168	SK-N-SH	brain:	n/a	n/a
18	PBX3	chr12:2373364-2374603	SK-N-SH	brain:	n/a	chr12:2373828-2373837
19	RCOR1	chr12:2373016-2375224	IMR90	lung:	n/a	n/a
20	GATA3	chr12:2373877-2375418	SK-N-SH	brain:	n/a	chr12:2374672-2374680 chr12:2375367-2375377
21	MAFK	chr12:2374104-2374494	IMR90	lung:	n/a	n/a
22	RXRA	chr12:2373862-2374617	SK-N-SH	brain:	n/a	chr12:2374342-2374361
23	POLR2A	chr12:2373980-2374459	SK-N-SH	brain:	n/a	n/a
24	NFIC	chr12:2373946-2374960	SK-N-SH	brain:	n/a	chr12:2374645-2374662 chr12:2374645-2374661
25	GATA3	chr12:2373202-2375520	SK-N-SH	brain:	n/a	chr12:2374672-2374680 chr12:2375367-2375377
26	TCF12	chr12:2373864-2375101	SK-N-SH	brain:	n/a	n/a
27	JUND	chr12:2373945-2374900	SK-N-SH	brain:	n/a	n/a
28	TEAD4	chr12:2373887-2374718	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr12:2373991-2374149	ProgFib	skin:	n/a	n/a
30	POLR2A	chr12:2372586-2374596	IMR90	lung:	n/a	n/a
31	RXRA	chr12:2373874-2374701	SK-N-SH	brain:	n/a	chr12:2374342-2374361
32	POLR2A	chr12:2372699-2375122	U87	brain:	n/a	n/a
33	POLR2A	chr12:2372346-2375668	U87	brain:	n/a	n/a
34	JUND	chr12:2373599-2375233	SK-N-SH	brain:	n/a	n/a
35	FOSL2	chr12:2373940-2374647	SK-N-SH	brain:	n/a	n/a
36	SIN3AK20	chr12:2374109-2374523	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr12:2373896-2374622	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:2373726..2376594-chr12:2378396..2380527,2	MCF-7	breast:
2	chr12:2373446..2375686-chr12:2379984..2382833,2	K562	blood:

Variant related genes	Relation type
CACNA1C-IT3	TF binding region
ENSG00000256721	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1006737	0.82[MEX][hapmap]
rs1860002	0.82[CEU][hapmap]
rs2007044	0.92[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs2159100	0.82[MEX][hapmap]
rs2238057	0.96[CEU][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2370414	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]
rs34382810	0.84[EUR][1000 genomes]
rs4765905	0.82[MEX][hapmap]
rs4765911	0.81[EUR][1000 genomes]
rs7297582	0.81[CEU][hapmap]
rs758170	0.82[MEX][hapmap]
rs882194	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs882195	0.83[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
rs2239038	AKAP3	cis	cerebellum	SCAN
rs2239038	CACNA1C	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2365200-2374200	Weak transcription	Brain Anterior Caudate	brain
2	chr12:2365400-2374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:2365400-2374400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:2365400-2374800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:2365400-2376000	Weak transcription	Brain Angular Gyrus	brain
6	chr12:2370000-2374400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:2370600-2375000	Enhancers	Right Ventricle	heart
8	chr12:2370600-2377400	Enhancers	Fetal Heart	heart
9	chr12:2370600-2378600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:2370800-2378800	Enhancers	NHLF	lung
11	chr12:2370800-2379200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:2371000-2380200	Enhancers	Left Ventricle	heart
13	chr12:2371200-2374400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:2372400-2379600	Enhancers	Colon Smooth Muscle	Colon
15	chr12:2372800-2374200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:2372800-2374800	Flanking Active TSS	Osteobl	bone
17	chr12:2372800-2378600	Enhancers	Rectal Smooth Muscle	rectum
18	chr12:2373000-2375000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:2373000-2375400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr12:2373000-2375600	Enhancers	Spleen	Spleen
21	chr12:2373000-2376000	Enhancers	Right Atrium	heart
22	chr12:2373200-2374200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:2373200-2374400	Enhancers	Fetal Muscle Trunk	muscle
24	chr12:2373200-2374600	Enhancers	Fetal Stomach	stomach
25	chr12:2373200-2374800	Enhancers	Placenta	Placenta
26	chr12:2373200-2375000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr12:2373200-2375400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:2373200-2377800	Enhancers	NH-A	brain
29	chr12:2373200-2378000	Enhancers	HSMM	muscle
30	chr12:2373200-2379000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:2373200-2379200	Enhancers	Aorta	Aorta
32	chr12:2373400-2375000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr12:2373400-2375200	Enhancers	Adipose Nuclei	Adipose
34	chr12:2373400-2375600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:2373600-2374800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:2373600-2375400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr12:2373800-2374200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:2373800-2374200	Weak transcription	Lung	lung
39	chr12:2373800-2374200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr12:2373800-2374200	Flanking Active TSS	HSMMtube	muscle
41	chr12:2373800-2374400	Enhancers	Fetal Intestine Large	intestine
42	chr12:2373800-2374800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr12:2373800-2374800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr12:2373800-2374800	Enhancers	Fetal Muscle Leg	muscle
45	chr12:2373800-2377800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr12:2373800-2378600	Enhancers	Fetal Intestine Small	intestine
47	chr12:2374000-2374200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr12:2374000-2374200	Enhancers	Brain Hippocampus Middle	brain
49	chr12:2374000-2374400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:2374000-2374800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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