Variant report

Variant	rs7315298
Chromosome Location	chr12:1912880-1912881
allele	C/T
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	chr12:1912790-1913012	HepG2	liver:	n/a	chr12:1912889-1912902 chr12:1912889-1912900

No.	Distal block	Cell Line	Cell type
1	chr12:1911026..1914378-chr12:2033211..2036733,3	MCF-7	breast:
2	chr12:1912567..1917043-chr12:1917472..1921043,5	K562	blood:
3	chr12:1912567..1914410-chr12:1917472..1919007,2	K562	blood:
4	chr12:1911095..1913405-chr12:2060628..2062758,2	MCF-7	breast:
5	chr12:1905522..1910417-chr12:1912711..1915784,4	K562	blood:

Variant related genes	Relation type
CACNA2D4	TF binding region
ENSG00000151062	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10128890	0.91[JPT][hapmap]
rs1044825	0.91[JPT][hapmap]
rs10744552	0.87[JPT][hapmap]
rs13219	0.91[JPT][hapmap]
rs2058111	0.90[JPT][hapmap]
rs2286379	0.91[JPT][hapmap]
rs3741971	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3741973	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766421	0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7294540	0.83[JPT][hapmap]
rs7300241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs758168	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv430442	chr12:1889823-1982151	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv556996	chr12:1891372-1934920	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1824001	chr12:1896738-1951940	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv898592	chr12:1901485-1937801	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv898593	chr12:1901485-1962759	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv468965	chr12:1907853-1931396	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv556997	chr12:1907853-1931396	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv468966	chr12:1907853-1933553	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv556998	chr12:1907853-1933553	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv470259	chr12:1907853-1945042	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7315298	RAD51AP1	cis	parietal	SCAN
rs7315298	CCR6	trans	lymphoblastoid	seeQTL
rs7315298	AKAP3	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1905600-1928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:1905800-1913400	Weak transcription	HepG2	liver
3	chr12:1906400-1913800	Weak transcription	Brain Angular Gyrus	brain
4	chr12:1906400-1913800	Weak transcription	Fetal Brain Male	brain
5	chr12:1906600-1913600	Weak transcription	Brain Anterior Caudate	brain
6	chr12:1906600-1913800	Weak transcription	Primary T cells from cord blood	blood
7	chr12:1906800-1913800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:1906800-1913800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:1906800-1913800	Weak transcription	Brain Substantia Nigra	brain
10	chr12:1906800-1914000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:1906800-1914000	Weak transcription	Right Atrium	heart
12	chr12:1906800-1915400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:1907000-1913800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:1907200-1913000	Weak transcription	Right Ventricle	heart
15	chr12:1907200-1913400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr12:1907200-1913800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr12:1907200-1913800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:1907600-1913600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:1907800-1913800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr12:1910000-1916400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:1910000-1916400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:1910400-1913800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:1910400-1913800	Weak transcription	Brain Germinal Matrix	brain
24	chr12:1910400-1913800	Weak transcription	Fetal Brain Female	brain
25	chr12:1910400-1914000	Weak transcription	Fetal Heart	heart
26	chr12:1910800-1913600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:1910800-1915000	Weak transcription	HSMMtube	muscle
28	chr12:1910800-1920000	Weak transcription	Primary B cells from cord blood	blood
29	chr12:1911000-1913800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:1911000-1913800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:1911200-1915400	Weak transcription	HSMM	muscle
32	chr12:1911400-1913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:1911600-1913400	Weak transcription	NHDF-Ad	bronchial
34	chr12:1911600-1919200	Weak transcription	Osteobl	bone
35	chr12:1911800-1913600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:1912000-1914000	Weak transcription	Spleen	Spleen
37	chr12:1912800-1914600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr12:1912800-1917000	Enhancers	Skeletal Muscle Female	skeletal muscle

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