Variant report

Variant	rs12988379
Chromosome Location	chr2:31509369-31509370
allele	G/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	chr2:31509081-31509482	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000213620	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1010477	0.91[ASN][1000 genomes]
rs10175943	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124256	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683836	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474941	1.00[ASN][1000 genomes]
rs2145036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366947	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951976	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4951977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952077	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952078	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs586245	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs590009	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs598204	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs602322	0.91[ASN][1000 genomes]
rs603214	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs604127	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs604986	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs610240	0.84[AFR][1000 genomes]
rs631396	0.91[ASN][1000 genomes]
rs637911	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644417	0.82[ASN][1000 genomes]
rs644736	0.82[ASN][1000 genomes]
rs646103	0.86[ASN][1000 genomes]
rs646200	0.86[ASN][1000 genomes]
rs6543622	1.00[ASN][1000 genomes]
rs661015	0.91[ASN][1000 genomes]
rs674791	0.91[ASN][1000 genomes]
rs684967	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7567147	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7581173	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9678585	0.89[EUR][1000 genomes]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12988379	NLRC4	cis	cerebellum	SCAN
rs12988379	IFT172	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31486600-31510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:31492800-31510600	Weak transcription	Aorta	Aorta
3	chr2:31495800-31509800	Weak transcription	Esophagus	oesophagus
4	chr2:31497000-31510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:31504600-31512800	Enhancers	Placenta	Placenta
6	chr2:31506200-31510000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:31507400-31511000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:31507600-31510200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:31507800-31510600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:31508200-31509400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:31508400-31509400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr2:31508800-31511200	Enhancers	NHEK	skin
13	chr2:31508800-31511600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:31508800-31511600	Enhancers	HUVEC	blood vessel
15	chr2:31509000-31510200	Enhancers	Fetal Heart	heart
16	chr2:31509000-31510400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:31509000-31510600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:31509000-31511000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:31509000-31511200	Enhancers	HMEC	breast
20	chr2:31509000-31511600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:31509200-31511200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr2:31509200-31522000	Weak transcription	H9 Cell Line	embryonic stem cell

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