Variant report

Variant	rs2373000
Chromosome Location	chr2:37592628-37592629
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	GATA3	chr2:37592607-37593248	MCF-7	breast:	n/a	n/a
2	GATA2	chr2:37592561-37592820	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr2:37592427-37593298	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr2:37592521-37592691	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37591915..37594227-chr2:37596693..37599097,2	MCF-7	breast:

Variant related genes	Relation type
QPCT	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10190959	0.92[YRI][hapmap]
rs1056021	0.82[JPT][hapmap]
rs11124569	0.82[JPT][hapmap]
rs1158218	0.80[LWK][hapmap]
rs1158219	0.80[LWK][hapmap]
rs12618410	0.82[JPT][hapmap]
rs17020479	1.00[YRI][hapmap]
rs2041836	1.00[YRI][hapmap]
rs2888434	0.86[JPT][hapmap]
rs3213745	0.92[YRI][hapmap]
rs3770754	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3770759	0.86[YRI][hapmap]
rs4998429	0.86[JPT][hapmap]
rs6734118	0.85[CHB][hapmap]
rs6743782	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430724	chr2:37546820-37628704	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv2685	chr2:37550096-37594923	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	23974872	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2373000	ATL2	cis	cerebellum	SCAN
rs2373000	CEBPZ	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37572600-37595400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:37577400-37607000	Weak transcription	Spleen	Spleen
3	chr2:37578200-37605400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:37578400-37604200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:37578600-37601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:37578800-37602200	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:37579800-37603000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:37580200-37603400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:37581600-37595600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:37583600-37607200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:37589200-37593800	Weak transcription	Esophagus	oesophagus
12	chr2:37589200-37602800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:37589800-37602800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:37590200-37594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:37591200-37593200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:37591400-37594000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:37591600-37595600	Weak transcription	Gastric	stomach
18	chr2:37591600-37598200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:37592200-37593400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:37592200-37595800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:37592400-37592800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr2:37592400-37593400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:37592400-37593400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:37592400-37593600	Enhancers	Osteobl	bone
25	chr2:37592400-37594200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:37592400-37594200	Enhancers	HSMM	muscle
27	chr2:37592400-37594400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:37592400-37594600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:37592400-37594600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:37592400-37594600	Enhancers	HSMMtube	muscle
31	chr2:37592600-37593200	Bivalent Enhancer	Primary T cells from cord blood	blood
32	chr2:37592600-37593400	Enhancers	NHDF-Ad	bronchial
33	chr2:37592600-37593600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:37592600-37593800	Bivalent Enhancer	GM12878-XiMat	blood
35	chr2:37592600-37594000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:37592600-37595800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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