Variant report

Variant	rs1042039
Chromosome Location	chr2:31558306-31558307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31555503..31558332-chr2:31561263..31563974,3	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10490361	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1054889	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12614330	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs169596	0.83[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs207429	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2268800	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736492	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs932559	0.92[ASW][hapmap];0.89[CEU][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv949028	chr2:31502801-31665108	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv2762446	chr2:31521093-31610311	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1042039	UCN	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31548000-31558400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:31548000-31634600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:31548400-31558600	Weak transcription	NHEK	skin
4	chr2:31553400-31559600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:31553600-31560200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:31555400-31558400	Weak transcription	NH-A	brain
7	chr2:31556000-31558800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:31556200-31558800	Weak transcription	Right Ventricle	heart
9	chr2:31556200-31559800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:31556200-31561000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:31556400-31558400	Weak transcription	Fetal Heart	heart
12	chr2:31556400-31558800	Genic enhancers	HMEC	breast
13	chr2:31556400-31561600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:31556600-31558600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:31556600-31559800	Enhancers	HSMMtube	muscle
16	chr2:31556600-31561600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:31556800-31558400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:31556800-31558600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:31556800-31558800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:31556800-31560400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:31556800-31561400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:31556800-31561600	Enhancers	HSMM	muscle
23	chr2:31557000-31558400	Weak transcription	NHDF-Ad	bronchial
24	chr2:31557200-31558800	Weak transcription	Fetal Intestine Small	intestine
25	chr2:31557200-31579600	Strong transcription	Liver	Liver
26	chr2:31557600-31558800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:31557600-31559200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:31557600-31560400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:31557600-31563600	Weak transcription	Gastric	stomach
30	chr2:31557800-31558800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:31557800-31558800	Weak transcription	NHLF	lung
32	chr2:31557800-31559400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:31558000-31558400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:31558000-31558400	Weak transcription	Osteobl	bone
35	chr2:31558200-31573200	Strong transcription	Fetal Intestine Large	intestine

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