Variant report

Variant	rs12459135
Chromosome Location	chr19:39886582-39886583
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	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
3	EGR1	chr19:39886540-39886760	K562	blood:	n/a	chr19:39886695-39886706 chr19:39886694-39886708 chr19:39886694-39886707 chr19:39886695-39886706 chr19:39886696-39886705 chr19:39886694-39886707 chr19:39886693-39886708 chr19:39886697-39886706 chr19:39886696-39886706 chr19:39886696-39886706
4	POLR2A	chr19:39886497-39886875	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39879787..39883867-chr19:39884525..39889123,13	K562	blood:

Variant related genes	Relation type
PAF1	TF binding region
ENSG00000063322	Chromatin interaction
ENSG00000006712	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1057745	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56138629	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58587357	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39883000-39888000	Weak transcription	Psoas Muscle	Psoas
2	chr19:39883000-39888200	Weak transcription	Right Atrium	heart
3	chr19:39883000-39888600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:39883000-39888600	Weak transcription	Small Intestine	intestine
5	chr19:39883000-39891800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:39883200-39887800	Weak transcription	HSMM	muscle
7	chr19:39883200-39888000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:39883200-39888000	Strong transcription	Fetal Intestine Small	intestine
9	chr19:39883200-39888200	Weak transcription	Fetal Heart	heart
10	chr19:39883200-39888200	Weak transcription	HUVEC	blood vessel
11	chr19:39883200-39888200	Weak transcription	NHEK	skin
12	chr19:39883200-39888600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:39883200-39891600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:39883200-39892400	Weak transcription	Fetal Brain Male	brain
15	chr19:39883200-39892400	Weak transcription	Fetal Kidney	kidney
16	chr19:39883400-39887000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:39883400-39887200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:39883400-39887800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr19:39883400-39888000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:39883400-39888000	Strong transcription	Fetal Stomach	stomach
21	chr19:39883400-39888200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:39883600-39886800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:39883600-39886800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:39883600-39886800	Strong transcription	Fetal Muscle Leg	muscle
25	chr19:39883600-39887000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:39883800-39886800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:39883800-39888000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr19:39884000-39886800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:39884000-39886800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:39884000-39886800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:39884000-39886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:39884000-39886800	Strong transcription	Fetal Brain Female	brain
33	chr19:39884000-39887000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr19:39884000-39887000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:39884000-39887000	Strong transcription	Adipose Nuclei	Adipose
36	chr19:39884000-39887400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr19:39884000-39888000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:39884000-39888000	Strong transcription	Fetal Intestine Large	intestine
39	chr19:39884000-39888000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr19:39884000-39888000	Strong transcription	Placenta	Placenta
41	chr19:39884000-39888000	Strong transcription	Thymus	Thymus
42	chr19:39884000-39888200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:39884200-39886600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr19:39884200-39886800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:39884200-39886800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:39884200-39886800	Strong transcription	Aorta	Aorta
47	chr19:39884200-39886800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr19:39884200-39886800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:39884200-39886800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr19:39884200-39886800	Strong transcription	Gastric	stomach

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