Variant report

Variant	rs57410428
Chromosome Location	chr2:55611475-55611476
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55597784..55600046-chr2:55608046..55611475,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10189439	0.92[ASN][1000 genomes]
rs11125567	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11680143	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11692239	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12470528	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12471421	0.82[ASN][1000 genomes]
rs12476508	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12476548	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12713292	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1344881	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1437394	0.93[ASN][1000 genomes]
rs1454421	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1545555	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1902059	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1982484	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1982485	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1992127	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992128	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2198577	0.82[ASN][1000 genomes]
rs2576687	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2576704	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576705	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576706	0.92[ASN][1000 genomes]
rs2576707	0.87[ASN][1000 genomes]
rs2576713	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2576714	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2576715	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2576716	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576717	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2589055	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589056	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589059	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589065	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589066	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2589072	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2589073	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589075	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589077	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2589084	0.85[ASN][1000 genomes]
rs2589085	0.93[ASN][1000 genomes]
rs2589087	0.93[ASN][1000 genomes]
rs2589088	0.93[ASN][1000 genomes]
rs2589090	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2589091	0.93[ASN][1000 genomes]
rs2589102	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589103	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2589105	0.93[ASN][1000 genomes]
rs2589106	0.93[ASN][1000 genomes]
rs2864828	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2864829	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2864830	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2867180	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2867181	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2903508	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2917776	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2917778	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920964	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920971	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920974	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2966467	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099075	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099076	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099077	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099079	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099082	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3099084	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3111404	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3111410	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3111411	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3111412	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3111413	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35963448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762510	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762512	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3791633	0.92[ASN][1000 genomes]
rs3791634	0.92[ASN][1000 genomes]
rs3791650	0.81[AFR][1000 genomes]
rs3791653	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4349381	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4672039	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55711116	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55828034	0.84[ASN][1000 genomes]
rs55908714	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56133422	0.84[ASN][1000 genomes]
rs61379198	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62137151	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62137154	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62137157	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62138071	0.82[ASN][1000 genomes]
rs6545487	0.92[ASN][1000 genomes]
rs6545488	0.92[ASN][1000 genomes]
rs6706178	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6718236	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6725124	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6727038	0.86[ASN][1000 genomes]
rs7425220	0.81[AMR][1000 genomes]
rs7561210	0.84[AMR][1000 genomes]
rs7564292	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7570934	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7575929	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7576695	0.91[ASN][1000 genomes]
rs7582580	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7586529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	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	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
rs57410428	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
2	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
3	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:55576000-55612200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
6	chr2:55579400-55614400	Weak transcription	Fetal Brain Female	brain
7	chr2:55579400-55622400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
9	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:55582800-55615000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:55584200-55612000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
14	chr2:55589600-55628800	Weak transcription	Fetal Thymus	thymus
15	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:55590400-55622400	Weak transcription	GM12878-XiMat	blood
17	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:55592200-55617600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:55592200-55631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:55592800-55615600	Weak transcription	NHEK	skin
22	chr2:55592800-55617800	Weak transcription	A549	lung
23	chr2:55592800-55626600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
25	chr2:55593000-55622400	Weak transcription	Brain Angular Gyrus	brain
26	chr2:55593000-55622400	Weak transcription	Brain Anterior Caudate	brain
27	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:55593400-55616400	Weak transcription	HUVEC	blood vessel
29	chr2:55593800-55631800	Weak transcription	Brain Germinal Matrix	brain
30	chr2:55598200-55616200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:55599200-55626800	Weak transcription	Osteobl	bone
32	chr2:55600000-55617600	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:55600600-55616200	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:55600600-55617400	Weak transcription	K562	blood
35	chr2:55600600-55617800	Weak transcription	Fetal Lung	lung
36	chr2:55600600-55631600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:55600800-55629400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:55600800-55629400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:55601200-55611800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:55601400-55612400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:55601800-55631000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:55602000-55618600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:55602000-55629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:55602200-55612000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:55602200-55615600	Weak transcription	Hela-S3	cervix
47	chr2:55602200-55629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:55602400-55617200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:55602400-55629600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:55603600-55629400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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