Variant report

Variant	rs3730256
Chromosome Location	chr19:40761212-40761213
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	chr19:40761110-40761326	HepG2	liver:	n/a	n/a
2	CTCF	chr19:40761140-40761290	HepG2	liver:	n/a	chr19:40761196-40761209
3	REST	chr19:40760704-40761838	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a
5	CTCF	chr19:40761120-40761270	Caco-2	colon:	n/a	chr19:40761196-40761209

Variant related genes	Relation type
AKT2	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11665880	0.94[ASN][1000 genomes]
rs268674	1.00[JPT][hapmap]
rs4150987	1.00[JPT][hapmap]

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	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1064502	chr19:40758049-40781360	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3730256	GPR4	cis	cerebellum	SCAN
rs3730256	EXOSC5	cis	cerebellum	SCAN
rs3730256	DMRTC2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40738000-40763800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr19:40750000-40763800	Strong transcription	Thymus	Thymus
3	chr19:40750000-40764000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr19:40751000-40761800	Weak transcription	Fetal Kidney	kidney
5	chr19:40751200-40761600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr19:40751200-40771200	Weak transcription	Fetal Heart	heart
7	chr19:40751800-40763600	Strong transcription	Fetal Stomach	stomach
8	chr19:40752600-40763400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:40752800-40763400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:40753000-40772000	Weak transcription	Fetal Brain Male	brain
11	chr19:40753200-40762800	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr19:40753200-40763000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:40753200-40763600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr19:40753200-40763800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:40753200-40764600	Strong transcription	Primary T cells from cord blood	blood
16	chr19:40753600-40763400	Strong transcription	Fetal Thymus	thymus
17	chr19:40753600-40763800	Strong transcription	Dnd41	blood
18	chr19:40753800-40763400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:40753800-40763800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr19:40753800-40764400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:40754000-40763000	Strong transcription	Brain Germinal Matrix	brain
22	chr19:40755000-40763200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:40755000-40763800	Strong transcription	Placenta	Placenta
24	chr19:40755200-40763600	Strong transcription	GM12878-XiMat	blood
25	chr19:40755400-40763600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr19:40755600-40762400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:40755600-40763000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:40755600-40764600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:40755800-40763000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:40755800-40763400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:40756000-40761800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:40756000-40762600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr19:40756000-40762800	Strong transcription	Spleen	Spleen
34	chr19:40756000-40763000	Strong transcription	Brain Angular Gyrus	brain
35	chr19:40756000-40763200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:40756000-40763600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:40756200-40763000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr19:40756400-40763200	Strong transcription	Fetal Brain Female	brain
39	chr19:40756800-40763400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr19:40757000-40763400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr19:40757200-40763000	Strong transcription	Brain Cingulate Gyrus	brain
42	chr19:40757200-40763000	Strong transcription	Fetal Lung	lung
43	chr19:40757200-40763200	Strong transcription	NHLF	lung
44	chr19:40757400-40763200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr19:40757400-40763400	Strong transcription	Primary B cells from cord blood	blood
46	chr19:40757600-40763000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr19:40757600-40763200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr19:40757600-40763200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr19:40757600-40763400	Strong transcription	A549	lung
50	chr19:40757800-40762600	Strong transcription	Aorta	Aorta

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