Variant report

Variant	rs2576687
Chromosome Location	chr2:55579488-55579489
allele	C/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..55581776-chr2:55584319..55586422,2	K562	blood:
2	chr2:55579484..55583558-chr2:55584922..55587594,3	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10189439	0.96[ASN][1000 genomes]
rs10865285	0.81[ASN][1000 genomes]
rs11125567	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11680143	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692239	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12470528	0.92[ASN][1000 genomes]
rs12471421	0.81[ASN][1000 genomes]
rs12476508	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12476548	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713292	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344881	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437394	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545555	0.88[ASN][1000 genomes]
rs1902059	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1982484	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982485	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1992127	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1992128	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198577	0.81[ASN][1000 genomes]
rs2576704	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576705	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576706	0.96[ASN][1000 genomes]
rs2576707	0.91[ASN][1000 genomes]
rs2576713	1.00[ASN][1000 genomes]
rs2576714	1.00[ASN][1000 genomes]
rs2576715	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2576716	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576717	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2589055	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2589056	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2589059	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589065	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589066	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589072	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589073	1.00[ASN][1000 genomes]
rs2589075	1.00[ASN][1000 genomes]
rs2589077	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2589084	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2589085	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589087	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589088	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589090	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589091	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589102	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589103	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589105	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589106	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864828	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864829	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864830	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867180	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2867181	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2903508	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2917776	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2917778	1.00[ASN][1000 genomes]
rs2920964	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920971	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920974	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2966467	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099075	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3099076	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099077	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099079	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099082	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099084	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111404	1.00[ASN][1000 genomes]
rs3111410	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3111411	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3111412	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111413	1.00[ASN][1000 genomes]
rs35963448	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3762510	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3791633	0.96[ASN][1000 genomes]
rs3791634	0.96[ASN][1000 genomes]
rs3791642	0.82[AFR][1000 genomes]
rs3791653	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4349381	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4672039	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55711116	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55828034	0.83[ASN][1000 genomes]
rs55908714	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56133422	0.83[ASN][1000 genomes]
rs57410428	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62137151	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62137154	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137157	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62138071	0.81[ASN][1000 genomes]
rs6545487	0.96[ASN][1000 genomes]
rs6545488	0.96[ASN][1000 genomes]
rs66507139	0.82[AMR][1000 genomes]
rs6706178	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6725124	0.85[ASN][1000 genomes]
rs6727038	0.90[ASN][1000 genomes]
rs7425220	0.81[EUR][1000 genomes]
rs7561210	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7564292	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7570934	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7575929	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7576695	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7582580	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586529	0.83[AMR][1000 genomes];0.95[ASN][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
rs2576687	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	chr2:55544200-55581800	Weak transcription	Left Ventricle	heart
14	chr2:55546200-55585000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:55547400-55590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:55548200-55585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:55554800-55584200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:55554800-55591600	Weak transcription	HSMMtube	muscle
19	chr2:55555000-55582200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:55555800-55586000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:55558400-55595000	Weak transcription	Fetal Heart	heart
23	chr2:55563600-55584400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:55564200-55605200	Weak transcription	Fetal Kidney	kidney
25	chr2:55564400-55582000	Weak transcription	Hela-S3	cervix
26	chr2:55570600-55582400	Weak transcription	NHLF	lung
27	chr2:55571400-55580200	Strong transcription	HSMM	muscle
28	chr2:55572000-55610200	Weak transcription	Liver	Liver
29	chr2:55573000-55582600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:55573800-55590800	Weak transcription	HUVEC	blood vessel
31	chr2:55574400-55579600	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:55574400-55583000	Strong transcription	Fetal Thymus	thymus
33	chr2:55574600-55591800	Weak transcription	HMEC	breast
34	chr2:55575200-55581800	Weak transcription	Ovary	ovary
35	chr2:55575200-55582000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:55575800-55581800	Weak transcription	Fetal Stomach	stomach
37	chr2:55576000-55612200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:55576800-55590800	Weak transcription	NH-A	brain
39	chr2:55577600-55584400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:55577800-55584600	Strong transcription	Dnd41	blood
41	chr2:55578000-55580400	Weak transcription	Colonic Mucosa	Colon
42	chr2:55578200-55584200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:55578400-55579600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:55578400-55580600	Strong transcription	HepG2	liver
45	chr2:55578400-55590600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:55578600-55579600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr2:55578600-55579600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr2:55578600-55579600	Strong transcription	Brain Angular Gyrus	brain
49	chr2:55578600-55579800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:55578600-55585200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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