Variant report

Variant	rs7247063
Chromosome Location	chr19:40321524-40321525
allele	A/C
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	SIN3AK20	chr19:40319989-40326136	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:40306432-40338982	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:40320301-40321966	A549	lung:	n/a	n/a
4	POLR2A	chr19:40320707-40321641	HL-60	blood:	n/a	n/a
5	POLR2A	chr19:40320911-40321747	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:40320116-40321604	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40321340..40326326-chr19:40333108..40338214,12	MCF-7	breast:

Variant related genes	Relation type
DYRK1B	TF binding region
ENSG00000105202	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1001974	0.80[CHB][hapmap]
rs10416495	1.00[ASN][1000 genomes]
rs10422280	0.81[GIH][hapmap]
rs11880094	0.81[GIH][hapmap]
rs11881344	0.83[EUR][1000 genomes]
rs12459589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459950	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12460804	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17709688	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2072290	0.81[GIH][hapmap]
rs2354471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810383	0.81[GIH][hapmap]
rs4802061	0.80[CHB][hapmap]
rs56021455	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56047603	0.98[ASN][1000 genomes]
rs56110449	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62106861	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62106862	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62106863	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718066	0.81[GIH][hapmap]
rs7250408	0.82[CHB][hapmap];0.88[GIH][hapmap]
rs7253739	0.81[GIH][hapmap]
rs7259470	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7507534	0.80[CHB][hapmap]
rs8111901	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7247063	MARK4	cis	cerebellum	SCAN
rs7247063	TOMM40	cis	cerebellum	SCAN
rs7247063	PHLDB3	cis	parietal	SCAN
rs7247063	PPP1R13L	cis	parietal	SCAN
rs7247063	APOC4	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40312000-40323200	Strong transcription	A549	lung
2	chr19:40315400-40322800	Strong transcription	Placenta	Placenta
3	chr19:40315800-40322200	Strong transcription	Placenta Amnion	Placenta Amnion
4	chr19:40315800-40322400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:40315800-40322400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:40315800-40322600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:40315800-40323400	Weak transcription	Right Atrium	heart
8	chr19:40315800-40323600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:40316000-40321800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
10	chr19:40316000-40321800	Strong transcription	Thymus	Thymus
11	chr19:40316000-40322000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:40316000-40322000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:40316000-40322200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:40316000-40322400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:40316000-40322400	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr19:40316000-40322400	Strong transcription	Lung	lung
17	chr19:40316000-40322600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:40316000-40322800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:40316000-40322800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:40316000-40322800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:40316000-40323000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:40316000-40323200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:40316000-40323200	Strong transcription	NHEK	skin
24	chr19:40316200-40321600	Weak transcription	Fetal Brain Male	brain
25	chr19:40316200-40321600	Strong transcription	Right Ventricle	heart
26	chr19:40316200-40321800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr19:40316200-40321800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:40316200-40322000	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr19:40316200-40322000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:40316200-40322200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:40316200-40322200	Strong transcription	Adipose Nuclei	Adipose
32	chr19:40316200-40322400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:40316200-40322400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:40316200-40322400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:40316200-40322400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr19:40316200-40322400	Strong transcription	Fetal Brain Female	brain
37	chr19:40316200-40322600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:40316200-40322600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:40316200-40322600	Strong transcription	Brain Cingulate Gyrus	brain
40	chr19:40316200-40322600	Strong transcription	Colon Smooth Muscle	Colon
41	chr19:40316200-40322800	Strong transcription	Fetal Stomach	stomach
42	chr19:40316200-40322800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:40316200-40323400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:40316400-40321600	Strong transcription	Left Ventricle	heart
45	chr19:40316400-40321600	Strong transcription	Pancreas	Pancrea
46	chr19:40316400-40321800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:40316400-40321800	Strong transcription	Esophagus	oesophagus
48	chr19:40316400-40322200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr19:40316400-40322200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr19:40316400-40322200	Weak transcription	Fetal Heart	heart

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