Variant report

Variant	rs12459566
Chromosome Location	chr19:18493295-18493296
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	POLR2A	chr19:18492725-18493607	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:18492587-18501908	HepG2	liver:	n/a	n/a
3	HEY1	chr19:18492693-18501831	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:18492743-18494398	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GDF15	TF binding region
MIR3189	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1055150	0.97[ASN][1000 genomes]
rs1059519	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12459782	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2059039	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3787023	0.99[ASN][1000 genomes]
rs3848646	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3848647	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3848648	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3848649	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4328570	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808128	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808789	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4808792	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808793	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808794	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55947999	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56033872	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6512262	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6512263	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6512264	0.99[EUR][1000 genomes]
rs6512265	1.00[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6512266	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7251610	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8101804	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107264	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer 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	92 gene(s)	inside rSNPs	diseases
6	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12459566	COMP	cis	cerebellum	SCAN
rs12459566	FAM32A	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18485800-18496600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr19:18485800-18499000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:18486400-18496600	Weak transcription	Fetal Kidney	kidney
4	chr19:18488600-18496800	Enhancers	Placenta	Placenta
5	chr19:18489800-18493600	Weak transcription	HSMM	muscle
6	chr19:18490000-18496200	Weak transcription	Gastric	stomach
7	chr19:18491400-18493600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:18491400-18494000	Weak transcription	Fetal Lung	lung
9	chr19:18491400-18495600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:18491400-18496200	Weak transcription	GM12878-XiMat	blood
11	chr19:18491400-18497400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:18491600-18493800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr19:18491600-18494000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:18491600-18495600	Weak transcription	NHEK	skin
15	chr19:18491600-18495800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:18491600-18496400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:18491600-18496400	Weak transcription	NHLF	lung
18	chr19:18491600-18497400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr19:18491800-18493600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:18491800-18493600	Weak transcription	K562	blood
21	chr19:18491800-18493800	Weak transcription	Fetal Muscle Leg	muscle
22	chr19:18491800-18494800	Enhancers	A549	lung
23	chr19:18491800-18495000	Weak transcription	Fetal Intestine Small	intestine
24	chr19:18491800-18495800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:18491800-18496000	Weak transcription	HMEC	breast
26	chr19:18491800-18496200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:18491800-18496400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:18491800-18496400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:18491800-18496400	Weak transcription	NHDF-Ad	bronchial
30	chr19:18491800-18496600	Weak transcription	Osteobl	bone
31	chr19:18491800-18496800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:18491800-18496800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:18491800-18496800	Weak transcription	Colonic Mucosa	Colon
34	chr19:18491800-18496800	Weak transcription	Right Atrium	heart
35	chr19:18491800-18497000	Weak transcription	Lung	lung
36	chr19:18492000-18493600	Weak transcription	Adipose Nuclei	Adipose
37	chr19:18492000-18493600	Weak transcription	Liver	Liver
38	chr19:18492000-18493600	Weak transcription	Stomach Mucosa	stomach
39	chr19:18492000-18493800	Weak transcription	Pancreas	Pancrea
40	chr19:18492000-18493800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:18492000-18495400	Weak transcription	Hela-S3	cervix
42	chr19:18492000-18496200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr19:18492000-18498800	Weak transcription	Right Ventricle	heart
44	chr19:18492600-18493400	Enhancers	Fetal Intestine Large	intestine
45	chr19:18492600-18493600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:18492600-18494200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:18492600-18494200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr19:18492600-18494800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:18492800-18493400	Enhancers	NH-A	brain
50	chr19:18492800-18493600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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