Variant report

Variant	rs5940539
Chromosome Location	chrX:154830650-154830651
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	chrX:154830345..154832030-chrX:154841051..154843638,2	MCF-7	breast:
2	chrX:154821010..154823368-chrX:154829376..154831463,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185973	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10782079	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1084450	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs473491	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs473529	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs473772	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs476928	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs479901	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs498000	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs561928	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs574386	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs580468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5940376	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs5940478	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs5940479	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs5940484	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs5940486	0.88[JPT][hapmap]
rs5940510	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs5983658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs5983743	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs628761	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs674707	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs89278	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv29972	chrX:154418093-154929412	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv532965	chrX:154418093-155226096	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv532967	chrX:154418093-155252027	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv915940	chrX:154577793-155232907	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv534441	chrX:154664337-155251871	Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv519485	chrX:154737376-154929412	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv869305	chrX:154739403-155190347	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv916736	chrX:154762193-155232894	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv520699	chrX:154774663-154929412	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154806000-154841000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chrX:154819200-154841200	Weak transcription	A549	lung
3	chrX:154826600-154831000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chrX:154827800-154834000	Weak transcription	Fetal Intestine Large	intestine
5	chrX:154830000-154834800	Weak transcription	Primary T cells from cord blood	blood
6	chrX:154830400-154831400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chrX:154830600-154830800	Enhancers	Esophagus	oesophagus

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