Variant report

Variant	rs516402
Chromosome Location	chr1:166569578-166569579
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:166566883..166568406-chr1:166568618..166571458,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10127508	0.81[ASN][1000 genomes]
rs10127625	0.81[ASN][1000 genomes]
rs1017506	0.81[ASN][1000 genomes]
rs10494467	0.81[ASN][1000 genomes]
rs12022279	0.81[ASN][1000 genomes]
rs1442502	0.81[ASN][1000 genomes]
rs1552905	0.81[ASN][1000 genomes]
rs1552906	0.81[ASN][1000 genomes]
rs1552907	0.81[ASN][1000 genomes]
rs1662067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16857521	0.81[ASN][1000 genomes]
rs2197148	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28606045	0.81[ASN][1000 genomes]
rs28808044	0.81[ASN][1000 genomes]
rs3904702	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs474189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs476074	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap]
rs482267	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486538	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs491367	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs505636	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs510265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514026	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs537629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs539246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs552888	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs555316	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs558874	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[YRI][hapmap]
rs565376	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs570565	0.87[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs578278	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61835399	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv2757759	chr1:166491879-166650985	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2758975	chr1:166491879-166650985	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv872511	chr1:166505186-166590046	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv872512	chr1:166532565-166581706	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv872513	chr1:166532565-166590046	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv872514	chr1:166532565-166595209	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv872515	chr1:166532565-166595692	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv872516	chr1:166536198-166590046	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv872517	chr1:166539001-166590046	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv2756869	chr1:166543542-166601778	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv872519	chr1:166545275-166616786	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv872518	chr1:166545275-166623180	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv34401	chr1:166546342-166617601	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv872520	chr1:166546851-166590046	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv872521	chr1:166568908-166593683	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs516402	CCDC81	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166559800-166569800	Weak transcription	K562	blood

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