Variant report

Variant	rs2589105
Chromosome Location	chr2:55582362-55582363
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55579484..55583558-chr2:55584922..55587594,3	K562	blood:

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10169395	0.81[AFR][1000 genomes]
rs10172058	0.81[AFR][1000 genomes]
rs10189439	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10496042	0.87[AFR][1000 genomes]
rs10865285	0.81[ASN][1000 genomes]
rs11125567	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11678347	0.82[AFR][1000 genomes]
rs11680143	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692239	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12470528	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12471421	0.81[ASN][1000 genomes]
rs12476508	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12476548	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12617887	0.86[AFR][1000 genomes]
rs12621289	0.87[AFR][1000 genomes]
rs12713292	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713293	0.81[AFR][1000 genomes]
rs12713294	0.81[AFR][1000 genomes]
rs12713295	0.81[AFR][1000 genomes]
rs13019339	0.84[AFR][1000 genomes]
rs13022424	0.87[AFR][1000 genomes]
rs1344881	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349884	0.81[AFR][1000 genomes]
rs1437394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545555	0.88[ASN][1000 genomes]
rs1902059	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1982484	0.91[ASN][1000 genomes]
rs1982485	0.87[ASN][1000 genomes]
rs1992127	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1992128	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198575	0.81[AFR][1000 genomes]
rs2198577	0.81[ASN][1000 genomes]
rs2576687	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576704	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576705	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576706	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2576707	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2576713	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2576714	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2576715	1.00[ASN][1000 genomes]
rs2576716	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576717	0.95[ASN][1000 genomes]
rs2589055	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2589056	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2589059	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589065	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589066	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589072	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589073	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2589075	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589084	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2589085	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589087	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589088	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589090	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589091	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589102	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589103	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589106	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864828	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864829	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864830	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867175	0.81[AFR][1000 genomes]
rs2867177	0.81[AFR][1000 genomes]
rs2867180	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2867181	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2903508	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2917776	0.96[ASN][1000 genomes]
rs2917778	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2920964	0.92[ASN][1000 genomes]
rs2920971	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920974	0.95[ASN][1000 genomes]
rs2966467	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099075	0.99[ASN][1000 genomes]
rs3099076	0.95[ASN][1000 genomes]
rs3099077	1.00[ASN][1000 genomes]
rs3099079	1.00[ASN][1000 genomes]
rs3099082	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099084	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111404	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111410	0.99[ASN][1000 genomes]
rs3111411	0.99[ASN][1000 genomes]
rs3111412	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111413	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35963448	0.95[ASN][1000 genomes]
rs3762510	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3791633	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3791634	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3791652	0.87[AFR][1000 genomes]
rs3791653	0.99[ASN][1000 genomes]
rs4349381	0.95[ASN][1000 genomes]
rs55711116	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55828034	0.83[ASN][1000 genomes]
rs55908714	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56133422	0.83[ASN][1000 genomes]
rs57410428	0.93[ASN][1000 genomes]
rs62137151	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62137154	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137157	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62138071	0.81[ASN][1000 genomes]
rs6545487	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6545488	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6706178	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6724338	0.91[AFR][1000 genomes]
rs6725124	0.85[ASN][1000 genomes]
rs6727038	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6754930	0.86[AFR][1000 genomes]
rs6756777	0.83[AFR][1000 genomes]
rs7561473	0.85[AFR][1000 genomes]
rs7564292	0.93[ASN][1000 genomes]
rs7570934	0.87[ASN][1000 genomes]
rs7575929	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7576695	0.95[ASN][1000 genomes]
rs7582580	1.00[ASN][1000 genomes]
rs7586529	0.95[ASN][1000 genomes]
rs7589390	0.81[AFR][1000 genomes]
rs9789365	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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
rs2589105	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
2	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
6	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
9	chr2:55537800-55609400	Weak transcription	Lung	lung
10	chr2:55541400-55584400	Weak transcription	Spleen	Spleen
11	chr2:55542400-55589800	Weak transcription	Fetal Intestine Large	intestine
12	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
13	chr2:55546200-55585000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:55547400-55590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:55548200-55585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:55554800-55584200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:55554800-55591600	Weak transcription	HSMMtube	muscle
18	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:55555800-55586000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:55558400-55595000	Weak transcription	Fetal Heart	heart
21	chr2:55563600-55584400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:55564200-55605200	Weak transcription	Fetal Kidney	kidney
23	chr2:55570600-55582400	Weak transcription	NHLF	lung
24	chr2:55572000-55610200	Weak transcription	Liver	Liver
25	chr2:55573000-55582600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:55573800-55590800	Weak transcription	HUVEC	blood vessel
27	chr2:55574400-55583000	Strong transcription	Fetal Thymus	thymus
28	chr2:55574600-55591800	Weak transcription	HMEC	breast
29	chr2:55576000-55612200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:55576800-55590800	Weak transcription	NH-A	brain
31	chr2:55577600-55584400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:55577800-55584600	Strong transcription	Dnd41	blood
33	chr2:55578200-55584200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr2:55578400-55590600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:55578600-55585200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:55579200-55585400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:55579200-55585400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:55579200-55591200	Weak transcription	NHEK	skin
39	chr2:55579200-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:55579200-55602200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
42	chr2:55579400-55582600	Weak transcription	Adipose Nuclei	Adipose
43	chr2:55579400-55582600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:55579400-55583000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:55579400-55584000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:55579400-55584200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:55579400-55586000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:55579400-55586200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:55579400-55586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:55579400-55588600	Weak transcription	Brain Cingulate Gyrus	brain

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