Variant report

Variant	rs2970556
Chromosome Location	chr1:209377775-209377776
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209376128..209379505-chr1:209382757..209384972,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11586407	0.82[ASN][1000 genomes]
rs11586451	0.84[ASN][1000 genomes]
rs12722814	0.82[ASN][1000 genomes]
rs12755287	0.82[ASN][1000 genomes]
rs1933612	0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs1933619	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap]
rs2266024	0.84[EUR][1000 genomes]
rs2489651	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788152	0.83[CEU][hapmap]
rs2788158	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2788159	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2788161	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788162	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788168	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788170	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970555	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970560	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2996683	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2996687	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2996688	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523921	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34944110	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4396124	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4402132	0.84[ASN][1000 genomes]
rs6658956	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6672407	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs66763810	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678963	0.82[ASN][1000 genomes]
rs6692414	0.84[ASN][1000 genomes]
rs6704132	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs71636106	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2970556	NUCKS1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209370400-209380800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209373200-209380800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:209373200-209381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:209373600-209380400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:209376200-209378200	Enhancers	Fetal Brain Female	brain
6	chr1:209376200-209378800	Enhancers	Fetal Brain Male	brain
7	chr1:209376800-209380400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:209377000-209380600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:209377000-209380800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:209377200-209381200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:209377400-209380800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:209377600-209377800	Enhancers	Brain Germinal Matrix	brain
13	chr1:209377600-209377800	Enhancers	Fetal Stomach	stomach
14	chr1:209377600-209380600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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