Variant report

Variant	rs1024582
Chromosome Location	chr12:2402246-2402247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:2398121..2403045-chr12:2403191..2406718,4	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1006737	0.92[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs10744560	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10774035	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10774036	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10774037	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs11062157	1.00[JPT][hapmap]
rs11062170	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12311439	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12315711	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2159100	0.92[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4298967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765905	0.92[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs4765913	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs4765914	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs758170	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs769087	0.92[CEU][hapmap];0.84[EUR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1024582	CACNA1C	cis	cerebellum	SCAN
rs1024582	EFCAB4B	cis	parietal	SCAN
rs1024582	SLC6A12	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2390600-2402800	Enhancers	Colon Smooth Muscle	Colon
2	chr12:2390600-2406800	Enhancers	Fetal Heart	heart
3	chr12:2391200-2402600	Enhancers	Rectal Smooth Muscle	rectum
4	chr12:2391800-2404000	Weak transcription	Brain Angular Gyrus	brain
5	chr12:2393800-2405600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:2393800-2409000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:2394000-2412200	Weak transcription	Colonic Mucosa	Colon
8	chr12:2396400-2402400	Enhancers	Spleen	Spleen
9	chr12:2396600-2406600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:2396800-2405600	Weak transcription	Pancreas	Pancrea
11	chr12:2397600-2403800	Weak transcription	Adipose Nuclei	Adipose
12	chr12:2397600-2404000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:2397800-2403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:2397800-2403800	Weak transcription	Osteobl	bone
15	chr12:2397800-2404000	Weak transcription	Fetal Lung	lung
16	chr12:2397800-2404000	Weak transcription	NH-A	brain
17	chr12:2398000-2403400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:2398000-2403400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:2398200-2403800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:2398200-2404000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:2398400-2403600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:2398400-2415000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:2398400-2415200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:2398600-2403400	Weak transcription	Placenta	Placenta
25	chr12:2398600-2403400	Weak transcription	HSMM	muscle
26	chr12:2398600-2403600	Weak transcription	Fetal Thymus	thymus
27	chr12:2398600-2404400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:2398600-2406000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:2398600-2410200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:2398800-2403600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:2398800-2404000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:2398800-2404800	Weak transcription	Fetal Brain Male	brain
33	chr12:2399000-2404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:2399000-2404000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:2399400-2403400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:2399600-2405200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:2399600-2413400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:2399800-2403600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:2399800-2403600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:2400000-2403400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:2400200-2403400	Weak transcription	NHDF-Ad	bronchial
42	chr12:2400200-2403800	Weak transcription	HSMMtube	muscle
43	chr12:2400400-2403200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:2400400-2403400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:2400400-2403400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:2400400-2403800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:2400600-2403000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:2400800-2403000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:2401000-2410800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:2401200-2402800	Enhancers	Stomach Smooth Muscle	stomach

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