Variant report

Variant	rs11683974
Chromosome Location	chr2:234613000-234613001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234474897..234476429-chr2:234612353..234614313,2	MCF-7	breast:
2	chr2:234393460..234398388-chr2:234612624..234620814,16	MCF-7	breast:
3	chr2:234610804..234613588-chr2:234613696..234615763,4	MCF-7	breast:
4	chr2:234473635..234475919-chr2:234612965..234615031,3	MCF-7	breast:
5	chr2:234470715..234472722-chr2:234612737..234614853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1054804	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11675168	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11676072	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11679312	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11684169	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11689628	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11691824	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11691827	0.95[EUR][1000 genomes]
rs11695770	0.95[EUR][1000 genomes]
rs12471326	1.00[CEU][hapmap]
rs28899194	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28899469	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28899472	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28900371	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs28900373	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28900379	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28900384	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28900385	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34622615	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45449995	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45454101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45510999	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60103279	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61296714	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6708136	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6740653	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6741543	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234602800-234614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:234609000-234614400	Weak transcription	Stomach Mucosa	stomach
3	chr2:234609000-234614800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:234609200-234614000	Weak transcription	NHEK	skin
5	chr2:234609200-234614200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:234610800-234613200	ZNF genes & repeats	A549	lung
7	chr2:234611000-234616000	Enhancers	Liver	Liver
8	chr2:234611400-234616600	Weak transcription	HUVEC	blood vessel
9	chr2:234611600-234614600	Weak transcription	Hela-S3	cervix
10	chr2:234611800-234614000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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