Variant report

Variant	rs10187983
Chromosome Location	chr2:55660508-55660509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55458753..55460899-chr2:55659427..55661705,2	MCF-7	breast:
2	chr2:55659643..55661172-chr2:55741607..55744341,2	MCF-7	breast:
3	chr2:55463171..55466180-chr2:55659869..55661423,3	MCF-7	breast:
4	chr2:55652771..55655244-chr2:55659480..55661281,2	K562	blood:
5	chr2:55653744..55655531-chr2:55659781..55661813,3	K562	blood:

Variant related genes	Relation type
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10169061	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10191937	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11125573	0.82[CHB][hapmap];0.88[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11886931	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11891739	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11902837	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12621495	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12623605	0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713293	0.80[AMR][1000 genomes]
rs12713294	0.80[AMR][1000 genomes]
rs12713296	0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12713298	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12991401	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13001912	0.80[AMR][1000 genomes]
rs13013113	0.80[AMR][1000 genomes]
rs13389156	0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13423775	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1349884	0.80[AMR][1000 genomes]
rs1349885	0.80[AMR][1000 genomes]
rs1902060	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2198575	0.80[AMR][1000 genomes]
rs2867176	0.80[AMR][1000 genomes]
rs28672687	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36052911	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828235	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56978967	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6746104	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6747649	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7589390	0.80[AMR][1000 genomes]
rs7604067	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7606505	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]

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
rs10187983	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55658400-55660600	Weak transcription	HepG2	liver

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