Variant report

Variant	rs10848568
Chromosome Location	chr12:1850384-1850385
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	chr12:1814200..1816471-chr12:1849026..1851387,2	MCF-7	breast:
2	chr12:1848455..1851151-chr12:1856944..1859382,3	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1058322	0.85[ASN][1000 genomes]
rs10734999	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap]
rs10735000	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744548	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10744549	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744550	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773979	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10773981	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10773987	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10848554	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832522	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11836547	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12296831	0.86[EUR][1000 genomes]
rs12370189	0.85[CHB][hapmap]
rs1468491	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs16928751	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1860054	0.81[EUR][1000 genomes]
rs1860055	0.81[EUR][1000 genomes]
rs2058112	0.84[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2286380	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs35854772	0.81[EUR][1000 genomes]
rs4140993	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4766414	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57216374	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60523400	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66673051	0.81[EUR][1000 genomes]
rs67365540	0.81[EUR][1000 genomes]
rs67405160	0.81[EUR][1000 genomes]
rs67567175	0.81[EUR][1000 genomes]
rs703176	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132184	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7134070	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7138701	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7302234	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs73040178	0.81[EUR][1000 genomes]
rs73040720	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311218	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs7316374	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7488369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs767870	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7954991	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7963224	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967137	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7975375	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9805042	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9805109	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9888418	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10848568	CACNA2D4	cis	multi-tissue	Pritchard
rs10848568	ANO2	cis	cerebellum	SCAN
rs10848568	KDM5A	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1816200-1857800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:1816200-1866400	Weak transcription	Esophagus	oesophagus
3	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
4	chr12:1817000-1856600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:1823000-1866600	Weak transcription	Gastric	stomach
6	chr12:1824000-1850400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:1824000-1866600	Weak transcription	HSMM	muscle
8	chr12:1825200-1855400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:1826000-1885400	Weak transcription	NH-A	brain
10	chr12:1828600-1855800	Weak transcription	Fetal Intestine Large	intestine
11	chr12:1831400-1857800	Weak transcription	Lung	lung
12	chr12:1834400-1850600	Weak transcription	Osteobl	bone
13	chr12:1836800-1855400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:1837000-1861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:1837200-1855400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:1840800-1852000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:1840800-1854000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:1840800-1855600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:1841800-1851400	Weak transcription	Brain Angular Gyrus	brain
20	chr12:1842400-1854200	Weak transcription	Dnd41	blood
21	chr12:1845600-1885200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:1846000-1851800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr12:1846000-1852200	Enhancers	HepG2	liver
24	chr12:1846200-1850800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:1846200-1851200	Enhancers	Stomach Mucosa	stomach
26	chr12:1846400-1850800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:1846600-1851400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:1847200-1851200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:1847200-1851400	Weak transcription	Brain Anterior Caudate	brain
30	chr12:1847200-1851800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:1847600-1854200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:1847600-1857800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:1847600-1863800	Weak transcription	Ovary	ovary
34	chr12:1847600-1885200	Weak transcription	Right Atrium	heart
35	chr12:1847800-1850600	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:1848200-1850600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:1848400-1851200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr12:1849000-1850600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:1849200-1850600	Enhancers	Primary B cells from peripheral blood	blood
40	chr12:1849200-1851000	Enhancers	Liver	Liver
41	chr12:1849200-1851600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr12:1849200-1851800	Enhancers	Adipose Nuclei	Adipose
43	chr12:1849200-1851800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr12:1849400-1850400	Enhancers	Duodenum Mucosa	Duodenum
45	chr12:1849400-1850400	Enhancers	Fetal Intestine Small	intestine
46	chr12:1849400-1850600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr12:1849400-1850600	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr12:1849400-1850600	Enhancers	Fetal Thymus	thymus
49	chr12:1849400-1850800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr12:1849400-1850800	Enhancers	Right Ventricle	heart

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