Variant report

Variant	rs12230440
Chromosome Location	chr12:1856953-1856954
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1856721..1858693-chr12:1863172..1864680,2	MCF-7	breast:
2	chr12:1848455..1851151-chr12:1856944..1859382,3	K562	blood:
3	chr12:1856328..1858670-chr12:1861251..1864008,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1029629	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs10848551	0.83[CHB][hapmap]
rs10848566	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11061918	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11061925	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs11061927	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs11061935	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[TSI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11061946	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11061952	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11061956	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11061962	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs11061967	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11061973	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11833054	0.82[ASN][1000 genomes]
rs12579507	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12581815	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12810020	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs12821401	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16928704	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2058033	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2058035	0.80[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs2370055	0.80[CHB][hapmap]
rs4766413	0.80[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs7132033	0.80[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs71454839	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7297509	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs73040715	0.85[ASN][1000 genomes]
rs73040736	0.87[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

Variant related diseases (count:1)

Disease	PMID	Source
Adverse response to lamotrigine and phenytoin	22379998	GWAS catalog

Chromatin state (count:74 , 50 per page) page: 1 2

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	chr12:1823000-1866600	Weak transcription	Gastric	stomach
5	chr12:1824000-1866600	Weak transcription	HSMM	muscle
6	chr12:1826000-1885400	Weak transcription	NH-A	brain
7	chr12:1831400-1857800	Weak transcription	Lung	lung
8	chr12:1837000-1861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:1845600-1885200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:1847600-1857800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:1847600-1863800	Weak transcription	Ovary	ovary
12	chr12:1847600-1885200	Weak transcription	Right Atrium	heart
13	chr12:1849800-1868400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:1849800-1868800	Weak transcription	Pancreas	Pancrea
15	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
16	chr12:1850000-1866600	Weak transcription	Fetal Lung	lung
17	chr12:1850200-1865800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:1850200-1885200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:1850400-1863400	Weak transcription	Fetal Stomach	stomach
20	chr12:1850400-1870400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
22	chr12:1850800-1863400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:1850800-1863400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:1850800-1885200	Weak transcription	Right Ventricle	heart
25	chr12:1851000-1863400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:1851000-1866400	Weak transcription	NHLF	lung
27	chr12:1851200-1858000	Weak transcription	Osteobl	bone
28	chr12:1851400-1857000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:1851400-1866600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr12:1851600-1858000	Weak transcription	Psoas Muscle	Psoas
31	chr12:1851600-1863400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:1851600-1866400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:1851800-1863400	Weak transcription	Thymus	Thymus
34	chr12:1851800-1863600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:1851800-1876600	Weak transcription	Stomach Mucosa	stomach
36	chr12:1854000-1858800	ZNF genes & repeats	GM12878-XiMat	blood
37	chr12:1854400-1864400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:1854600-1859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:1854600-1863400	Weak transcription	Adipose Nuclei	Adipose
40	chr12:1854600-1863400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:1854600-1870400	Weak transcription	HSMMtube	muscle
42	chr12:1854800-1858200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:1855200-1858200	Weak transcription	Brain Substantia Nigra	brain
44	chr12:1855200-1861800	Weak transcription	Brain Anterior Caudate	brain
45	chr12:1855600-1857400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
46	chr12:1855600-1858000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:1855600-1858600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:1855600-1858600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:1855600-1863400	Weak transcription	Left Ventricle	heart
50	chr12:1855800-1857400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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