Variant report

Variant	rs58708869
Chromosome Location	chr2:55629313-55629314
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr2:55629287-55629763	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55627632..55629326-chr2:55632488..55634437,2	K562	blood:
2	chr2:55624788..55628704-chr2:55629085..55632054,3	K562	blood:
3	chr2:55629189..55632200-chr2:55632234..55637417,4	K562	blood:

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10184756	0.93[AFR][1000 genomes]
rs11125568	0.88[AFR][1000 genomes]
rs11125569	0.89[AFR][1000 genomes]
rs13008631	0.81[AFR][1000 genomes]
rs1454415	0.89[AFR][1000 genomes]
rs1454419	0.89[AFR][1000 genomes]
rs2045134	0.90[AFR][1000 genomes]
rs2045135	0.92[AFR][1000 genomes]
rs2045136	0.86[AFR][1000 genomes]
rs2219130	0.89[AFR][1000 genomes]
rs28498550	0.81[AMR][1000 genomes]
rs2867178	0.90[AFR][1000 genomes]
rs2867179	0.92[AFR][1000 genomes]
rs2903509	0.93[AFR][1000 genomes]
rs4277563	0.92[AFR][1000 genomes]
rs4672034	0.88[AFR][1000 genomes]
rs4672035	0.89[AFR][1000 genomes]
rs4672040	0.93[AFR][1000 genomes]
rs56201519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6545492	0.85[AFR][1000 genomes]
rs6705104	0.88[AFR][1000 genomes]
rs6709204	0.93[AFR][1000 genomes]
rs6720698	0.89[AFR][1000 genomes]
rs6733814	0.91[AFR][1000 genomes]
rs7559987	0.88[AFR][1000 genomes]
rs7574743	0.89[AFR][1000 genomes]
rs7579037	0.92[AFR][1000 genomes]
rs7589279	0.92[AFR][1000 genomes]
rs7602189	0.89[AFR][1000 genomes]
rs7603105	0.92[AFR][1000 genomes]
rs9751964	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv275364	chr2:55621732-55632233	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:79 , 50 per page) page: 1 2

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	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
8	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:55592200-55631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
13	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:55593800-55631800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:55600600-55631600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:55600800-55629400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:55600800-55629400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:55601800-55631000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:55602000-55629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:55602200-55629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:55602400-55629600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:55603600-55629400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:55603600-55630200	Weak transcription	NH-A	brain
25	chr2:55606200-55630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:55608600-55630400	Weak transcription	HSMM	muscle
27	chr2:55612600-55629600	Weak transcription	Dnd41	blood
28	chr2:55612600-55630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:55612800-55632000	Weak transcription	Fetal Stomach	stomach
30	chr2:55614200-55632000	Weak transcription	Thymus	Thymus
31	chr2:55616600-55635400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:55616600-55635400	Weak transcription	HMEC	breast
33	chr2:55616800-55630200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:55616800-55632200	Weak transcription	Hela-S3	cervix
35	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
36	chr2:55618200-55635200	Weak transcription	Psoas Muscle	Psoas
37	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
39	chr2:55618600-55636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:55619000-55630200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:55619000-55632200	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:55619200-55629400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:55619200-55636800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:55619600-55630400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:55619600-55632000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:55622600-55630400	Weak transcription	K562	blood
47	chr2:55623000-55635600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
49	chr2:55623600-55629400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:55623600-55630200	Weak transcription	Brain Cingulate Gyrus	brain

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