Variant report

Variant	rs10840141
Chromosome Location	chr11:8902218-8902219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8704114..8705703-chr11:8902100..8903899,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10743093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743095	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10769947	0.81[CEU][hapmap]
rs10769948	0.81[CEU][hapmap]
rs10769957	0.81[CEU][hapmap]
rs10769967	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10769968	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10769971	0.86[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10769973	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769979	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10840130	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs10840134	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840136	0.81[EUR][1000 genomes]
rs10840142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840147	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042078	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs11042082	0.81[EUR][1000 genomes]
rs11042088	0.81[EUR][1000 genomes]
rs11042102	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042125	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042149	0.81[CEU][hapmap]
rs11042151	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11042154	0.93[CEU][hapmap];0.81[JPT][hapmap]
rs1109305	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1123936	0.85[CEU][hapmap]
rs11603841	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs12224436	0.82[CEU][hapmap]
rs1529641	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1560569	0.93[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1569408	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1883098	0.97[EUR][1000 genomes]
rs1980428	0.85[CEU][hapmap]
rs1980429	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1984791	0.81[JPT][hapmap]
rs1988708	0.95[EUR][1000 genomes]
rs1988709	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016942	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2568043	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2568045	0.85[CEU][hapmap]
rs2568054	0.96[EUR][1000 genomes]
rs2568059	0.96[EUR][1000 genomes]
rs2568061	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568062	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568065	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568090	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2653567	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2653570	0.81[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2653593	0.96[EUR][1000 genomes]
rs2653605	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2653606	0.81[EUR][1000 genomes]
rs2653607	0.82[EUR][1000 genomes]
rs2653613	0.81[EUR][1000 genomes]
rs2653616	0.96[EUR][1000 genomes]
rs2742480	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2742536	0.82[CEU][hapmap]
rs2742537	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2742540	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2742545	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs2742550	0.96[EUR][1000 genomes]
rs2742552	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs34842234	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36192694	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4554887	0.81[EUR][1000 genomes]
rs4909952	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4910062	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4910119	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910156	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910157	0.87[ASN][1000 genomes]
rs4910158	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4910200	0.84[EUR][1000 genomes]
rs4910442	0.81[CEU][hapmap]
rs4929911	0.81[CEU][hapmap]
rs4929912	0.81[CEU][hapmap]
rs4929914	0.81[CEU][hapmap]
rs4929922	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs61876187	0.81[EUR][1000 genomes]
rs6486060	0.85[CEU][hapmap]
rs7118463	0.81[EUR][1000 genomes]
rs7119939	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7123429	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7123861	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7479407	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7925728	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7930026	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs7937298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7943377	0.80[EUR][1000 genomes]
rs7945705	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7947631	0.83[CEU][hapmap]
rs905290	0.80[CEU][hapmap]
rs978636	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10840141	C11orf17	cis	multi-tissue	Pritchard
rs10840141	AKIP1	cis	Thyroid	GTEx
rs10840141	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs10840141	TMEM9B-AS1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8892800-8906600	Weak transcription	Spleen	Spleen
2	chr11:8894000-8903400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:8901000-8908000	Weak transcription	Psoas Muscle	Psoas
4	chr11:8901800-8905000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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