Variant report

Variant	rs2589073
Chromosome Location	chr2:55567692-55567693
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10189439	0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10865285	0.81[ASN][1000 genomes]
rs11125567	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11680143	0.86[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692239	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12470528	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12471421	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs12476508	0.88[ASN][1000 genomes]
rs12476548	0.92[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12614357	0.91[AFR][1000 genomes]
rs12713292	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019339	0.84[YRI][hapmap]
rs1344881	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1370360	0.89[YRI][hapmap];0.91[AFR][1000 genomes]
rs1437394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1454421	0.83[EUR][1000 genomes]
rs1545555	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1902059	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1982484	0.91[ASN][1000 genomes]
rs1982485	0.87[ASN][1000 genomes]
rs1992127	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1992128	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198577	0.81[ASN][1000 genomes]
rs2576687	1.00[ASN][1000 genomes]
rs2576704	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576705	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576706	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2576707	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2576713	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576714	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576716	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576717	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2589055	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2589056	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2589059	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589065	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589066	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589072	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589075	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589077	0.96[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589084	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2589085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2589086	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2589087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2589088	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2589090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2589091	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2589102	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589103	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589105	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2589106	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2864828	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2864829	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864830	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867180	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2867181	0.91[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2903508	0.88[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2917776	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2917778	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920964	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920971	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2966467	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099075	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3099076	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099077	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3099084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3111404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111410	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3111411	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3111412	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35963448	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762510	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3762512	0.85[EUR][1000 genomes]
rs3791633	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3791634	0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3791653	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4349381	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672039	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs55711116	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55828034	0.83[ASN][1000 genomes]
rs55908714	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56133422	0.83[ASN][1000 genomes]
rs57410428	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61379198	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62137151	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62137154	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137157	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62138071	0.81[ASN][1000 genomes]
rs6545487	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6545488	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6545493	0.88[JPT][hapmap]
rs6706178	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6718236	0.84[EUR][1000 genomes]
rs6725124	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6727038	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7558687	0.85[YRI][hapmap]
rs7564292	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7570934	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7575929	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7576695	0.95[ASN][1000 genomes]
rs7582580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586529	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7603216	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2589073	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
3	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
4	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
6	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
9	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
12	chr2:55537800-55609400	Weak transcription	Lung	lung
13	chr2:55539200-55567800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:55539200-55579000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:55539200-55579000	Weak transcription	NHEK	skin
16	chr2:55541400-55584400	Weak transcription	Spleen	Spleen
17	chr2:55541800-55574800	Weak transcription	Ovary	ovary
18	chr2:55542400-55589800	Weak transcription	Fetal Intestine Large	intestine
19	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
20	chr2:55544200-55581800	Weak transcription	Left Ventricle	heart
21	chr2:55546200-55585000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:55546600-55579000	Weak transcription	K562	blood
23	chr2:55546800-55578800	Weak transcription	GM12878-XiMat	blood
24	chr2:55547400-55590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:55548200-55585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:55548600-55574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:55548800-55570000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:55548800-55574800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:55551800-55577000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:55553400-55577200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:55554600-55577200	Weak transcription	Placenta	Placenta
32	chr2:55554800-55584200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:55554800-55591600	Weak transcription	HSMMtube	muscle
34	chr2:55555000-55582200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:55555200-55569800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:55555200-55574400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:55555200-55578800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:55555800-55570400	Weak transcription	Liver	Liver
40	chr2:55555800-55586000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:55556600-55579000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:55557000-55578600	Weak transcription	Brain Angular Gyrus	brain
43	chr2:55558000-55578600	Weak transcription	Brain Substantia Nigra	brain
44	chr2:55558200-55570800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:55558400-55571600	Weak transcription	Fetal Brain Female	brain
46	chr2:55558400-55595000	Weak transcription	Fetal Heart	heart
47	chr2:55559200-55578800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:55560400-55578800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:55560600-55575000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr2:55560600-55578800	Weak transcription	Fetal Brain Male	brain

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