Variant report

Variant	rs10984009
Chromosome Location	chr9:100618660-100618661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100617184..100619335-chr9:100637041..100639858,3	MCF-7	breast:
2	chr9:100614821..100616567-chr9:100616970..100619601,2	MCF-7	breast:
3	chr9:100602066..100604948-chr9:100618492..100620676,2	K562	blood:

Variant related genes	Relation type
ENSG00000178919	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10512256	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs1059003	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs10983845	1.00[ASN][1000 genomes]
rs10983892	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983893	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983896	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984098	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984377	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10984516	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs10984522	0.92[CEU][hapmap]
rs10984532	1.00[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs10984545	0.86[CEU][hapmap]
rs12156487	0.82[EUR][1000 genomes]
rs12375612	1.00[CEU][hapmap]
rs12377722	1.00[ASN][1000 genomes]
rs13295123	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348387	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1443433	1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs17687621	1.00[CEU][hapmap]
rs1947015	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4742708	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs4743143	0.82[EUR][1000 genomes]
rs4743144	1.00[CEU][hapmap]
rs4743149	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs6478403	1.00[ASN][1000 genomes]
rs7032302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043516	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs721417	1.00[ASN][1000 genomes]
rs72751594	1.00[ASN][1000 genomes]
rs72751597	1.00[ASN][1000 genomes]
rs72753506	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753508	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753537	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72753557	0.82[EUR][1000 genomes]
rs7851498	0.87[CEU][hapmap]
rs7854948	1.00[CEU][hapmap]
rs7860766	1.00[ASN][1000 genomes]
rs7871887	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs925487	1.00[CHD][hapmap]

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	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10984009	ZNF782	cis	parietal	SCAN
rs10984009	C9orf156	cis	cerebellum	SCAN
rs10984009	GALNT12	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100613400-100618800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:100617600-100620000	Weak transcription	Pancreas	Pancrea
3	chr9:100617800-100619200	Weak transcription	A549	lung

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