Variant report

Variant	rs17103858
Chromosome Location	chr11:105024039-105024040
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 188 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:178)

rs_ID	r²[population]
rs10502046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10502047	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11606407	1.00[CHB][hapmap]
rs12281540	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12416756	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12417470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12419220	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420524	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421544	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12421898	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12787184	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12796365	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797290	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797775	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12798696	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12800151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12801987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12806837	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503386	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503391	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1503395	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699089	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1699090	1.00[ASN][1000 genomes]
rs17103597	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17103670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17103773	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103781	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103836	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103866	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103873	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103951	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17103953	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17376473	1.00[CHB][hapmap]
rs17376738	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17377910	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17378343	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17446518	1.00[CHB][hapmap]
rs1792749	1.00[ASN][1000 genomes]
rs1792774	1.00[ASN][1000 genomes]
rs1847301	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047840	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047841	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062807	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062808	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409065	0.92[EUR][1000 genomes]
rs3181184	1.00[CHB][hapmap]
rs3181327	1.00[CHB][hapmap]
rs3181328	1.00[CHB][hapmap]
rs3181330	1.00[CHB][hapmap]
rs3181334	1.00[CHB][hapmap]
rs34105770	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34146979	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34212668	0.92[EUR][1000 genomes]
rs34255114	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34806541	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34819285	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35120805	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35136587	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35394521	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35560124	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35565964	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35743576	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35995863	1.00[ASN][1000 genomes]
rs473394	1.00[ASN][1000 genomes]
rs473549	1.00[ASN][1000 genomes]
rs475266	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754122	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754123	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754124	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754125	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4755076	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4755077	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4755078	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4755079	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4755080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4755081	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476889	1.00[ASN][1000 genomes]
rs481736	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs481926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483345	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs484626	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs486123	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs486537	1.00[ASN][1000 genomes]
rs486641	1.00[ASN][1000 genomes]
rs487128	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488992	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs489715	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs490565	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs492366	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs492519	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492859	1.00[ASN][1000 genomes]
rs492981	1.00[ASN][1000 genomes]
rs493426	1.00[ASN][1000 genomes]
rs493814	1.00[ASN][1000 genomes]
rs498892	1.00[ASN][1000 genomes]
rs500577	1.00[ASN][1000 genomes]
rs501192	1.00[ASN][1000 genomes]
rs501394	1.00[ASN][1000 genomes]
rs501429	1.00[ASN][1000 genomes]
rs501626	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs503153	1.00[ASN][1000 genomes]
rs504054	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs505901	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs507438	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs507509	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs508149	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516255	1.00[ASN][1000 genomes]
rs516286	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs517736	1.00[ASN][1000 genomes]
rs518878	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs518993	1.00[ASN][1000 genomes]
rs519047	1.00[ASN][1000 genomes]
rs520001	1.00[ASN][1000 genomes]
rs524048	1.00[ASN][1000 genomes]
rs526167	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs528076	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs529649	1.00[ASN][1000 genomes]
rs530009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs531542	1.00[ASN][1000 genomes]
rs531604	1.00[ASN][1000 genomes]
rs533050	1.00[ASN][1000 genomes]
rs533436	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534338	1.00[ASN][1000 genomes]
rs534811	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs535566	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536909	1.00[ASN][1000 genomes]
rs537014	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs538984	1.00[ASN][1000 genomes]
rs539595	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs542226	1.00[ASN][1000 genomes]
rs542571	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs542774	1.00[ASN][1000 genomes]
rs545911	1.00[ASN][1000 genomes]
rs546210	1.00[ASN][1000 genomes]
rs546449	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs548785	1.00[ASN][1000 genomes]
rs552134	1.00[ASN][1000 genomes]
rs554344	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs555301	1.00[ASN][1000 genomes]
rs556205	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs557905	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs558315	1.00[ASN][1000 genomes]
rs560880	1.00[ASN][1000 genomes]
rs567303	0.89[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568910	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs571593	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs572031	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs572687	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs572980	1.00[ASN][1000 genomes]
rs573440	1.00[ASN][1000 genomes]
rs580253	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs58131087	0.92[EUR][1000 genomes]
rs60235102	0.92[EUR][1000 genomes]
rs67513506	1.00[ASN][1000 genomes]
rs67835723	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692897	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs692914	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7117758	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123277	1.00[CHB][hapmap]
rs71484389	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484390	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484391	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484394	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484399	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484400	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484401	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484402	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928549	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7929852	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930712	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949293	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv468862	chr11:104774014-105243371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv556218	chr11:104774014-105243371	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv3385159	chr11:104786549-105051555	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1044970	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv541160	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv949337	chr11:104950007-105510193	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv975866	chr11:104994182-105034480	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv528789	chr11:105014564-105133046	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1045900	chr11:105015999-105138877	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17103858	COP1	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105010600-105026400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:105022600-105024400	Enhancers	Hela-S3	cervix
3	chr11:105023400-105024400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:105023600-105026400	Weak transcription	HUVEC	blood vessel
5	chr11:105023800-105024400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:105023800-105024400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:105024000-105024400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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