Variant report

Variant	rs3745764
Chromosome Location	chr19:37854580-37854581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1128327	1.00[JPT][hapmap]
rs11673646	1.00[YRI][hapmap]
rs12459637	1.00[YRI][hapmap]
rs12462271	0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12986074	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12986146	0.89[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17243193	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17303301	1.00[JPT][hapmap]
rs2279150	1.00[JPT][hapmap]
rs256741	0.87[AFR][1000 genomes]
rs34490389	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35828893	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3826849	1.00[ASW][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3745764	RABAC1	cis	cerebellum	SCAN
rs3745764	ZNF233	cis	parietal	SCAN
rs3745764	CATSPERG	cis	parietal	SCAN
rs3745764	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37826600-37856200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:37826600-37861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:37828000-37855800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:37841200-37855200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:37842600-37855400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr19:37842800-37856600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:37843800-37855800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:37843800-37857600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr19:37844000-37857000	ZNF genes & repeats	Liver	Liver
10	chr19:37845400-37855800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr19:37845600-37855800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:37846200-37856400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:37846400-37854600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
14	chr19:37847800-37854800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:37848200-37855200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:37848600-37855200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr19:37849000-37854600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
18	chr19:37849000-37854800	Strong transcription	Fetal Stomach	stomach
19	chr19:37849200-37857000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:37850000-37854800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:37850000-37855200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:37850000-37855200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
23	chr19:37850000-37855600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr19:37850000-37856800	ZNF genes & repeats	A549	lung
25	chr19:37850200-37854800	Strong transcription	Osteobl	bone
26	chr19:37850200-37855400	ZNF genes & repeats	GM12878-XiMat	blood
27	chr19:37850200-37856000	Strong transcription	Fetal Lung	lung
28	chr19:37850600-37855200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:37850600-37855200	Strong transcription	Brain Cingulate Gyrus	brain
30	chr19:37850600-37855400	Strong transcription	Brain Anterior Caudate	brain
31	chr19:37851000-37854600	Strong transcription	Fetal Kidney	kidney
32	chr19:37851000-37856400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:37851000-37856600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr19:37851600-37854800	Strong transcription	Pancreatic Islets	Pancreatic Islet
35	chr19:37851600-37856000	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr19:37852000-37854800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:37852000-37855000	Strong transcription	Aorta	Aorta
38	chr19:37852000-37855000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
39	chr19:37852000-37855200	ZNF genes & repeats	Esophagus	oesophagus
40	chr19:37852000-37855400	ZNF genes & repeats	Lung	lung
41	chr19:37852000-37855800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:37852200-37855000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
43	chr19:37852200-37855200	Strong transcription	Right Ventricle	heart
44	chr19:37852200-37855200	ZNF genes & repeats	Spleen	Spleen
45	chr19:37852200-37855600	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr19:37852200-37855600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:37852200-37857000	ZNF genes & repeats	Dnd41	blood
48	chr19:37852400-37854800	Strong transcription	Colon Smooth Muscle	Colon
49	chr19:37852400-37854800	Strong transcription	Fetal Brain Female	brain
50	chr19:37852400-37855400	Strong transcription	Brain Hippocampus Middle	brain

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