Variant report

Variant	rs9300298
Chromosome Location	chr12:1866204-1866205
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1798163..1800510-chr12:1865299..1867613,2	K562	blood:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1044471	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs10735003	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10744551	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10773980	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10773988	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10773989	0.89[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs10773991	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848548	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10848550	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs10848557	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10848561	0.85[ASN][1000 genomes]
rs10848563	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10848565	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10848567	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10848571	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061971	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612383	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs11614639	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs12316367	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2068485	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2068491	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2190556	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286383	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286384	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759374	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140992	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4765843	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765844	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766415	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489326	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138924	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs7294668	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296521	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7955261	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs7974422	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974924	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976827	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978362	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7978783	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9739162	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9805049	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv983262	chr12:1864626-1867474	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9300298	CACNA2D4	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 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	chr12:1847600-1885200	Weak transcription	Right Atrium	heart
8	chr12:1849800-1868400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:1849800-1868800	Weak transcription	Pancreas	Pancrea
10	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
11	chr12:1850000-1866600	Weak transcription	Fetal Lung	lung
12	chr12:1850200-1885200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:1850400-1870400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
15	chr12:1850800-1885200	Weak transcription	Right Ventricle	heart
16	chr12:1851000-1866400	Weak transcription	NHLF	lung
17	chr12:1851400-1866600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:1851600-1866400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:1851800-1876600	Weak transcription	Stomach Mucosa	stomach
20	chr12:1854600-1870400	Weak transcription	HSMMtube	muscle
21	chr12:1856000-1866400	Weak transcription	HUVEC	blood vessel
22	chr12:1856600-1872000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:1857200-1866400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:1857200-1870000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:1857200-1892800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:1857200-1893400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:1857400-1868000	Weak transcription	Fetal Brain Female	brain
28	chr12:1858200-1866400	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:1858200-1866400	Weak transcription	Lung	lung
30	chr12:1858200-1866400	Weak transcription	Spleen	Spleen
31	chr12:1858400-1868000	Weak transcription	Osteobl	bone
32	chr12:1858400-1869800	Weak transcription	NHDF-Ad	bronchial
33	chr12:1859200-1866600	Weak transcription	Psoas Muscle	Psoas
34	chr12:1860400-1869600	Weak transcription	K562	blood
35	chr12:1861600-1869800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:1862000-1894800	Weak transcription	Colonic Mucosa	Colon
37	chr12:1862600-1866400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:1862600-1866600	Weak transcription	Brain Anterior Caudate	brain
39	chr12:1862600-1874200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:1862800-1866400	Weak transcription	Brain Angular Gyrus	brain
41	chr12:1863000-1868400	Strong transcription	Dnd41	blood
42	chr12:1863000-1882000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:1863200-1867800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:1863200-1869600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:1863200-1869600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:1863400-1866800	Weak transcription	Brain Germinal Matrix	brain
47	chr12:1863400-1867000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:1863400-1867200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:1863400-1867200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr12:1863400-1867200	Strong transcription	Liver	Liver

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