Variant report

Variant	rs7588510
Chromosome Location	chr2:180732409-180732410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180724511..180728493-chr2:180729164..180732918,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221240	Chromatin interaction
ENSG00000144331	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10183495	0.96[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs10185471	0.96[CEU][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10195952	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10205122	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12328338	0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs13398994	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs13399189	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs13399303	0.84[CEU][hapmap]
rs13407401	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13410767	0.84[CEU][hapmap]
rs13418648	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs1351416	0.96[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1480706	0.91[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1480707	0.96[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1486234	0.84[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs16867014	0.84[CEU][hapmap];0.85[MEX][hapmap]
rs16867045	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs1906012	0.88[CEU][hapmap]
rs2219670	0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs259845	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4894128	0.83[CEU][hapmap]
rs4894130	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55875326	0.82[AMR][1000 genomes]
rs56090330	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56351245	0.82[AMR][1000 genomes]
rs6433810	0.80[EUR][1000 genomes]
rs6750809	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570985	0.91[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7573137	0.96[CEU][hapmap]
rs7585592	0.88[CEU][hapmap]
rs7601013	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs7603617	0.85[MEX][hapmap];0.89[TSI][hapmap]
rs7607354	0.91[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs966440	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428731	chr2:180629389-180805171	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7588510	HOXD13	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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