Variant report

Variant	rs12787853
Chromosome Location	chr11:86490519-86490520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:86450780..86453510-chr11:86484513..86491302,5	MCF-7	breast:
2	chr11:86385294..86387589-chr11:86488948..86490956,2	MCF-7	breast:
3	chr11:86487706..86491157-chr11:86492024..86495551,4	MCF-7	breast:
4	chr11:86447300..86456471-chr11:86483287..86490697,27	MCF-7	breast:
5	chr11:86485881..86490658-chr11:86500006..86503115,5	MCF-7	breast:
6	chr11:86483713..86491421-chr11:86509174..86514607,12	MCF-7	breast:
7	chr11:86346719..86349845-chr11:86488350..86491309,3	MCF-7	breast:
8	chr11:86482891..86485610-chr11:86489751..86491616,2	K562	blood:
9	chr11:86484180..86486892-chr11:86490481..86492650,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10501629	1.00[CHB][hapmap]
rs10898531	1.00[CHB][hapmap]
rs10898535	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234753	1.00[CHB][hapmap]
rs11234765	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11234767	1.00[CHB][hapmap]
rs11234768	1.00[CHB][hapmap]
rs11234778	1.00[CHB][hapmap]
rs11234798	1.00[CHB][hapmap]
rs11234799	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11234804	1.00[ASW][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234805	0.85[CEU][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234806	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234818	1.00[CHB][hapmap]
rs11602353	1.00[CHB][hapmap]
rs11602721	1.00[ASN][1000 genomes]
rs11606902	1.00[ASN][1000 genomes]
rs11607392	1.00[CHB][hapmap]
rs11608167	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12360547	1.00[CHB][hapmap]
rs12362094	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12786875	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12788554	1.00[ASN][1000 genomes]
rs12791740	1.00[CHB][hapmap]
rs12793595	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12799567	1.00[ASN][1000 genomes]
rs12805405	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs17149343	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs17159941	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17758195	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17758206	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17758334	1.00[CHB][hapmap]
rs17758376	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17758400	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17820139	1.00[CHB][hapmap]
rs1815753	1.00[CHB][hapmap]
rs1939118	1.00[ASN][1000 genomes]
rs2000537	1.00[ASN][1000 genomes]
rs2000538	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2105587	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs2186617	1.00[ASN][1000 genomes]
rs34873514	1.00[ASN][1000 genomes]
rs34906001	0.85[AFR][1000 genomes]
rs3781614	1.00[ASN][1000 genomes]
rs4363628	0.92[ASW][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap]
rs6592313	1.00[CHB][hapmap]
rs6592314	1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102870	0.94[YRI][hapmap];0.92[AFR][1000 genomes]
rs7105597	1.00[CHB][hapmap]
rs7128682	1.00[CHB][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128805	1.00[CHB][hapmap]
rs71465661	0.92[AFR][1000 genomes]
rs744293	0.94[AFR][1000 genomes]
rs750789	1.00[ASN][1000 genomes]
rs754490	1.00[ASN][1000 genomes]
rs7937881	0.87[EUR][1000 genomes]
rs872619	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1049157	chr11:86409059-86504155	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv521505	chr11:86438115-86515072	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv2756074	chr11:86456552-86729552	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12787853	CCDC89	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86487400-86501400	Weak transcription	Ovary	ovary
2	chr11:86487800-86495000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:86489600-86491800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:86490200-86493800	Weak transcription	Hela-S3	cervix

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