Variant report

Variant	rs17122742
Chromosome Location	chr1:62199300-62199301
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62189181..62192315-chr1:62198499..62200681,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162604	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10493311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11539585	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11802679	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11805607	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13375232	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1353424	1.00[EUR][1000 genomes]
rs17122675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17122684	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17122726	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1890262	1.00[EUR][1000 genomes]
rs2051137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57862885	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57901641	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61285999	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6678289	0.84[YRI][hapmap]
rs6698090	1.00[EUR][1000 genomes]
rs72925623	1.00[EUR][1000 genomes]
rs72925628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925658	1.00[AMR][1000 genomes]
rs72925685	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925687	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72927617	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72927635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7544197	1.00[EUR][1000 genomes]
rs7551993	1.00[EUR][1000 genomes]
rs7554012	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17122742	TM2D1	cis	multi-tissue	Pritchard
rs17122742	BBP	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62191400-62207400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:62198400-62199600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:62198400-62199800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr1:62198800-62199400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:62199200-62199600	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:62199200-62200000	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:62199200-62200000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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