Variant report

Variant	rs56320407
Chromosome Location	chr2:55633205-55633206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55629189..55632200-chr2:55632234..55637417,4	K562	blood:
2	chr2:55633136..55639027-chr2:55639441..55643745,9	K562	blood:
3	chr2:55627632..55629326-chr2:55632488..55634437,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11125567	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11680143	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11692239	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12471421	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12476508	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12476548	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713292	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1545555	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1902059	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1982484	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1982485	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1992127	0.80[EUR][1000 genomes]
rs1992128	0.80[EUR][1000 genomes]
rs2198577	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2576704	0.82[EUR][1000 genomes]
rs2576716	0.82[EUR][1000 genomes]
rs2589059	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2589065	0.82[EUR][1000 genomes]
rs2589072	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2589102	0.84[EUR][1000 genomes]
rs2589103	0.83[EUR][1000 genomes]
rs2864828	0.84[AFR][1000 genomes]
rs2864829	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2867180	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2867181	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2903508	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2920971	0.82[EUR][1000 genomes]
rs3762510	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4672039	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55711116	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55828034	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55908714	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56133422	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61379198	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62137151	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62137154	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62137157	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62138071	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6545493	0.81[AMR][1000 genomes]
rs6706178	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6718236	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725124	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7425220	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7561210	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7570934	0.80[ASN][1000 genomes]
rs7575929	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][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	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56320407	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	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
4	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
6	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
9	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:55616600-55635400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:55616600-55635400	Weak transcription	HMEC	breast
12	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
13	chr2:55618200-55635200	Weak transcription	Psoas Muscle	Psoas
14	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
16	chr2:55618600-55636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:55619200-55636800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:55623000-55635600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
20	chr2:55624200-55635600	Weak transcription	NHEK	skin
21	chr2:55624400-55645600	Weak transcription	Ovary	ovary
22	chr2:55627800-55636000	Weak transcription	NHDF-Ad	bronchial
23	chr2:55628600-55646000	Weak transcription	Esophagus	oesophagus
24	chr2:55629000-55634400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:55629000-55635600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:55629400-55633800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:55629400-55634400	Strong transcription	Fetal Thymus	thymus
28	chr2:55629600-55633800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:55629600-55633800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:55629600-55634200	Strong transcription	Dnd41	blood
31	chr2:55629600-55636200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:55630200-55634000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:55630200-55634200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:55630200-55634200	Enhancers	Brain Substantia Nigra	brain
35	chr2:55630200-55634800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:55630400-55634200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:55630400-55645800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr2:55630600-55633600	Strong transcription	Osteobl	bone
39	chr2:55630600-55644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:55630800-55635400	Weak transcription	NH-A	brain
41	chr2:55630800-55642400	Weak transcription	Pancreas	Pancrea
42	chr2:55630800-55644800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr2:55630800-55645200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:55630800-55645200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:55631000-55633400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:55631000-55633800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:55631000-55639000	Weak transcription	A549	lung
48	chr2:55631000-55645400	Weak transcription	Placenta	Placenta
49	chr2:55631200-55635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:55631200-55636400	Weak transcription	K562	blood

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