Variant report

Variant	rs2058112
Chromosome Location	chr12:1862158-1862159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1856328..1858670-chr12:1861251..1864008,2	K562	blood:
2	chr12:1794172..1796468-chr12:1859826..1862181,2	K562	blood:
3	chr12:1853793..1856029-chr12:1861433..1863477,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10735000	0.85[EUR][1000 genomes]
rs10744549	0.85[EUR][1000 genomes]
rs10744550	0.88[EUR][1000 genomes]
rs10773981	0.81[EUR][1000 genomes]
rs10773987	0.86[EUR][1000 genomes]
rs10848554	0.83[EUR][1000 genomes]
rs10848568	0.84[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs11832522	0.81[EUR][1000 genomes]
rs12296831	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468491	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928751	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860054	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860055	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286380	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35854772	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766414	0.85[EUR][1000 genomes]
rs57216374	0.84[EUR][1000 genomes]
rs57414925	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60523400	0.86[EUR][1000 genomes]
rs66673051	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67365540	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67405160	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67567175	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703176	0.82[EUR][1000 genomes]
rs7132184	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73040178	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73040720	0.81[EUR][1000 genomes]
rs73040763	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73041873	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7316374	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488369	0.83[CEU][hapmap]
rs767870	0.84[CEU][hapmap]
rs7963224	0.84[EUR][1000 genomes]
rs7967137	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975375	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs9805042	0.91[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs9805109	0.90[EUR][1000 genomes]
rs9888418	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv1038425	chr12:1857052-1902302	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2058112	ANO2	cis	cerebellum	SCAN
rs2058112	CACNA2D4	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1816200-1866400	Weak transcription	Esophagus	oesophagus
2	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
3	chr12:1823000-1866600	Weak transcription	Gastric	stomach
4	chr12:1824000-1866600	Weak transcription	HSMM	muscle
5	chr12:1826000-1885400	Weak transcription	NH-A	brain
6	chr12:1845600-1885200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:1847600-1863800	Weak transcription	Ovary	ovary
8	chr12:1847600-1885200	Weak transcription	Right Atrium	heart
9	chr12:1849800-1868400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:1849800-1868800	Weak transcription	Pancreas	Pancrea
11	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
12	chr12:1850000-1866600	Weak transcription	Fetal Lung	lung
13	chr12:1850200-1865800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:1850200-1885200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:1850400-1863400	Weak transcription	Fetal Stomach	stomach
16	chr12:1850400-1870400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
18	chr12:1850800-1863400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:1850800-1863400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:1850800-1885200	Weak transcription	Right Ventricle	heart
21	chr12:1851000-1863400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:1851000-1866400	Weak transcription	NHLF	lung
23	chr12:1851400-1866600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:1851600-1863400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:1851600-1866400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:1851800-1863400	Weak transcription	Thymus	Thymus
27	chr12:1851800-1863600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:1851800-1876600	Weak transcription	Stomach Mucosa	stomach
29	chr12:1854400-1864400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:1854600-1863400	Weak transcription	Adipose Nuclei	Adipose
31	chr12:1854600-1863400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:1854600-1870400	Weak transcription	HSMMtube	muscle
33	chr12:1855600-1863400	Weak transcription	Left Ventricle	heart
34	chr12:1855800-1862200	Weak transcription	Brain Hippocampus Middle	brain
35	chr12:1856000-1866400	Weak transcription	HUVEC	blood vessel
36	chr12:1856600-1872000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:1857000-1863400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:1857000-1863800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:1857200-1863000	Weak transcription	Dnd41	blood
40	chr12:1857200-1863400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:1857200-1863400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:1857200-1863400	Weak transcription	NHEK	skin
43	chr12:1857200-1863600	Weak transcription	Primary T cells from cord blood	blood
44	chr12:1857200-1864400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:1857200-1864600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:1857200-1865800	Weak transcription	Primary B cells from cord blood	blood
47	chr12:1857200-1866400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:1857200-1870000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:1857200-1892800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:1857200-1893400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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