Variant report

Variant	rs555259
Chromosome Location	chr11:84761929-84761930
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:84760678..84762987-chr11:84764753..84766897,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10501586	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10792792	0.88[CEU][hapmap]
rs10792794	0.92[CEU][hapmap];0.93[YRI][hapmap]
rs10898336	0.88[CEU][hapmap]
rs10898343	0.88[CEU][hapmap]
rs10898359	0.87[ASN][1000 genomes]
rs10898360	0.94[YRI][hapmap]
rs11234273	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs11234289	0.84[ASW][hapmap];0.83[YRI][hapmap]
rs11823251	0.81[AFR][1000 genomes]
rs1227842	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1227843	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1237921	0.83[CEU][hapmap]
rs1238728	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1377302	0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs1377303	0.82[JPT][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs1452928	0.82[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs1823777	0.84[ASW][hapmap];0.83[YRI][hapmap]
rs1826613	0.84[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs1940122	0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap]
rs1940123	0.88[CEU][hapmap]
rs1940133	0.88[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2155410	0.88[CEU][hapmap]
rs2155411	0.88[CEU][hapmap]
rs2155412	0.88[CEU][hapmap]
rs2252376	0.81[EUR][1000 genomes]
rs2253167	0.88[CEU][hapmap]
rs2444254	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2444255	0.88[CEU][hapmap]
rs2453151	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2509053	0.88[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2509056	0.81[CEU][hapmap]
rs2513242	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3862779	0.88[CEU][hapmap]
rs490286	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs527389	0.88[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs542892	0.92[ASW][hapmap];0.96[CEU][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs543740	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs555156	1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs560214	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs560587	0.82[EUR][1000 genomes]
rs567594	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs568330	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs568641	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs573650	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs574671	0.88[CEU][hapmap]
rs575189	0.88[CEU][hapmap]
rs577950	0.88[CEU][hapmap]
rs578782	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs582884	0.92[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs589093	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs592166	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs592622	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[YRI][hapmap]
rs593800	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs594122	0.83[EUR][1000 genomes]
rs595435	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs596556	0.88[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs597592	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs601375	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs605652	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs607864	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs613265	0.92[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs613315	0.92[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap]
rs617231	0.96[CEU][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs621007	0.88[CEU][hapmap]
rs625495	0.88[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs626013	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs626531	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs626700	0.92[CEU][hapmap];0.94[YRI][hapmap]
rs630948	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs631370	0.88[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs632351	0.83[EUR][1000 genomes]
rs633562	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635032	0.88[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs641655	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs641958	0.88[CEU][hapmap]
rs643891	0.88[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs646324	0.87[CEU][hapmap]
rs648506	0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs649468	0.84[CEU][hapmap]
rs650374	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs651661	0.88[CEU][hapmap]
rs652830	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658749	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs6592215	0.88[CEU][hapmap]
rs6592216	0.88[CEU][hapmap]
rs6592221	0.88[CEU][hapmap]
rs6592222	0.88[CEU][hapmap]
rs660274	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs666735	0.96[CEU][hapmap];0.86[AMR][1000 genomes]
rs670998	0.88[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs675160	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs675217	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs675255	0.87[CEU][hapmap]
rs679745	0.84[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs685294	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs686009	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs687695	0.88[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs688329	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs689226	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs694142	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs7102107	0.84[ASW][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs7110248	1.00[YRI][hapmap]
rs7118119	0.84[ASW][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs7126522	1.00[YRI][hapmap]
rs7127990	0.88[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7948646	0.84[ASW][hapmap];0.83[YRI][hapmap]
rs9634002	0.82[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs9634003	0.82[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs9634004	0.82[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs9634018	0.84[ASW][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]

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	nsv948410	chr11:83918339-84812001	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1048051	chr11:84419442-84784233	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv541109	chr11:84419442-84784233	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv430415	chr11:84661652-84833852	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1055097	chr11:84672444-84810441	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1040393	chr11:84708402-84866594	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv527535	chr11:84724795-84895033	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv528491	chr11:84724795-84895033	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1044370	chr11:84748993-85293233	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs555259	ANKRD42	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:84756400-84762800	Weak transcription	Fetal Brain Female	brain
2	chr11:84761400-84762200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:84761400-84762200	Enhancers	H9 Cell Line	embryonic stem cell
4	chr11:84761600-84762000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr11:84761600-84762200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr11:84761600-84762200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr11:84761800-84762200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr11:84761800-84762200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr11:84761800-84762400	Enhancers	HUES64 Cell Line	embryonic stem cell

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