Variant report

Variant	rs4570601
Chromosome Location	chr11:86486059-86486060
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:86380098..86384314-chr11:86483853..86489131,7	MCF-7	breast:
2	chr11:86450780..86453510-chr11:86484513..86491302,5	MCF-7	breast:
3	chr11:86447300..86456471-chr11:86483287..86490697,27	MCF-7	breast:
4	chr11:86485881..86490658-chr11:86500006..86503115,5	MCF-7	breast:
5	chr11:86483713..86491421-chr11:86509174..86514607,12	MCF-7	breast:
6	chr11:86414473..86417898-chr11:86484349..86489062,8	MCF-7	breast:
7	chr11:86485371..86486957-chr11:86491547..86493299,2	MCF-7	breast:
8	chr11:86484180..86486892-chr11:86490481..86492650,2	MCF-7	breast:
9	chr11:86463047..86464957-chr11:86484717..86487462,2	K562	blood:
10	chr11:86480465..86482047-chr11:86485833..86487935,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction
ENSG00000151376	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1075702	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10792875	0.81[EUR][1000 genomes]
rs10898534	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11234795	0.84[ASN][1000 genomes]
rs11234809	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11601553	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11602695	0.81[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs12361769	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12366016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12420039	0.82[CHB][hapmap]
rs12421517	0.83[ASN][1000 genomes]
rs12421942	0.87[ASN][1000 genomes]
rs12797648	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12802848	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12809023	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17211926	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17819068	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17819134	0.82[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs17819181	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs17819187	0.82[CHB][hapmap]
rs1807014	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1939110	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1939111	0.82[CHB][hapmap]
rs1939112	0.87[CHB][hapmap]
rs1939113	0.81[CHB][hapmap]
rs1939114	0.82[CHB][hapmap]
rs1939115	0.84[ASN][1000 genomes]
rs1939116	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1939117	0.97[ASN][1000 genomes]
rs1954769	0.86[JPT][hapmap]
rs2155081	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs2433409	0.82[CHB][hapmap]
rs2433427	0.82[CHB][hapmap]
rs2433429	0.81[CHB][hapmap]
rs2433433	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2433434	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2433435	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2433436	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2433438	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2433439	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2512996	0.81[CHB][hapmap]
rs2512997	0.81[CHB][hapmap]
rs2513018	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs3096715	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs3096716	0.86[JPT][hapmap]
rs34833002	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35902217	0.97[ASN][1000 genomes]
rs36061072	0.97[ASN][1000 genomes]
rs3809048	0.82[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4128368	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4245427	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4269941	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4304806	0.82[CHB][hapmap]
rs4307743	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4423210	0.82[CHB][hapmap]
rs4450192	0.87[ASN][1000 genomes]
rs4485132	0.86[CHB][hapmap]
rs4495915	0.98[ASN][1000 genomes]
rs4943958	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4943959	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4943960	0.88[ASN][1000 genomes]
rs4944630	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4944631	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944632	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944633	0.90[ASN][1000 genomes]
rs4944634	0.88[ASN][1000 genomes]
rs55646317	0.96[ASN][1000 genomes]
rs58823830	0.81[ASN][1000 genomes]
rs58976693	0.96[ASN][1000 genomes]
rs59850783	0.88[ASN][1000 genomes]
rs60023003	0.89[ASN][1000 genomes]
rs61690902	0.84[ASN][1000 genomes]
rs61707378	0.96[ASN][1000 genomes]
rs6592315	0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7105467	0.96[ASN][1000 genomes]
rs7120185	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120320	0.92[ASN][1000 genomes]
rs7123349	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7126492	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7131625	0.82[CHB][hapmap]
rs744292	0.96[ASN][1000 genomes]
rs7926235	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7926713	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7926946	0.84[ASN][1000 genomes]
rs7927257	0.84[ASN][1000 genomes]
rs7927479	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7940201	0.94[ASN][1000 genomes]
rs7942344	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7948063	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7950776	0.87[ASN][1000 genomes]
rs7951582	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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
rs4570601	CCDC89	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86484000-86486400	Enhancers	Hela-S3	cervix
2	chr11:86484800-86487200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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