Variant report

Variant	rs2198577
Chromosome Location	chr2:55659333-55659334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55644901..55646531-chr2:55657733..55659340,2	MCF-7	breast:
2	chr2:55652880..55655236-chr2:55657266..55660173,3	MCF-7	breast:
3	chr2:55645665..55649753-chr2:55657366..55660139,6	K562	blood:
4	chr2:55462241..55464416-chr2:55656583..55659722,3	MCF-7	breast:
5	chr2:55647253..55647758-chr2:55659096..55659834,2	K562	blood:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10865285	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125567	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11680143	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11692239	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12471421	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476508	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12476548	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713292	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1344881	0.81[ASN][1000 genomes]
rs1437394	0.81[ASN][1000 genomes]
rs1454421	0.82[AMR][1000 genomes]
rs1545555	0.87[ASN][1000 genomes]
rs1902059	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1982484	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1982485	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2576687	0.81[ASN][1000 genomes]
rs2576713	0.81[ASN][1000 genomes]
rs2576714	0.81[ASN][1000 genomes]
rs2576715	0.81[ASN][1000 genomes]
rs2589059	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2589065	0.81[ASN][1000 genomes]
rs2589072	0.81[AMR][1000 genomes]
rs2589073	0.81[ASN][1000 genomes]
rs2589075	0.81[ASN][1000 genomes]
rs2589085	0.81[ASN][1000 genomes]
rs2589087	0.81[ASN][1000 genomes]
rs2589088	0.81[ASN][1000 genomes]
rs2589090	0.81[ASN][1000 genomes]
rs2589091	0.81[ASN][1000 genomes]
rs2589102	0.81[ASN][1000 genomes]
rs2589103	0.81[ASN][1000 genomes]
rs2589105	0.81[ASN][1000 genomes]
rs2589106	0.81[ASN][1000 genomes]
rs2864828	0.81[ASN][1000 genomes]
rs2864829	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2864830	0.81[ASN][1000 genomes]
rs2867180	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2867181	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2903508	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2917778	0.81[ASN][1000 genomes]
rs2920971	0.81[ASN][1000 genomes]
rs2966467	0.81[ASN][1000 genomes]
rs3099077	0.81[ASN][1000 genomes]
rs3099079	0.81[ASN][1000 genomes]
rs3099082	0.81[ASN][1000 genomes]
rs3099084	0.81[ASN][1000 genomes]
rs3111404	0.81[ASN][1000 genomes]
rs3111410	0.82[ASN][1000 genomes]
rs3111411	0.82[ASN][1000 genomes]
rs3111412	0.81[ASN][1000 genomes]
rs3111413	0.81[ASN][1000 genomes]
rs35963448	0.83[ASN][1000 genomes]
rs3762510	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3762512	0.84[AMR][1000 genomes]
rs3791653	0.82[ASN][1000 genomes]
rs4349381	0.83[ASN][1000 genomes]
rs4672039	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55711116	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55828034	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55908714	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56133422	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs56162919	0.93[AMR][1000 genomes]
rs56320407	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs57410428	0.82[ASN][1000 genomes]
rs62137151	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62137154	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62137157	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62138071	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6545493	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706178	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6725124	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7425220	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7561210	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7564292	0.82[ASN][1000 genomes]
rs7570934	0.86[ASN][1000 genomes]
rs7575929	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7582580	0.81[ASN][1000 genomes]
rs7586529	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2198577	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55655200-55659400	Enhancers	Hela-S3	cervix
2	chr2:55658400-55660600	Weak transcription	HepG2	liver
3	chr2:55659000-55659400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:55659000-55659400	Enhancers	Adipose Nuclei	Adipose
5	chr2:55659000-55659400	Enhancers	A549	lung
6	chr2:55659000-55659600	Enhancers	Liver	Liver

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