Variant report

Variant	rs11891739
Chromosome Location	chr2:55662803-55662804
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10169061	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10187983	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10191937	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10496042	0.80[CEU][hapmap]
rs11125573	0.81[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11886931	0.85[CEU][hapmap];0.85[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11902837	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614357	0.80[AMR][1000 genomes]
rs12617887	0.81[AMR][1000 genomes]
rs12621289	0.81[CEU][hapmap]
rs12621495	0.81[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12623605	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713293	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12713294	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12713295	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12713296	0.80[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713298	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991401	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13001912	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13010237	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13010255	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13013113	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13019339	0.80[CEU][hapmap]
rs13022424	0.81[AMR][1000 genomes]
rs13389156	1.00[CEU][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13423775	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1349884	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1349885	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1370360	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs1902060	0.80[CEU][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2198575	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2867174	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2867175	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2867176	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28672687	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36052911	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791650	0.81[CEU][hapmap]
rs3791652	0.87[CEU][hapmap]
rs3828235	0.80[CEU][hapmap];0.88[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56978967	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66882175	0.81[EUR][1000 genomes]
rs6746104	0.81[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6747649	0.80[CEU][hapmap];0.88[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6752182	0.81[EUR][1000 genomes]
rs6756777	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs74181227	0.81[EUR][1000 genomes]
rs7572492	0.80[EUR][1000 genomes]
rs7589390	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7604067	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7606505	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9789365	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv961778	chr2:55659501-55668562	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11891739	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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