Variant report

Variant	rs55999882
Chromosome Location	chr2:172296782-172296783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172288399..172297381-chr2:172370978..172381493,22	K562	blood:
2	chr2:172294486..172297106-chr2:172372290..172374923,2	K562	blood:
3	chr2:172012919..172015830-chr2:172294656..172296953,2	K562	blood:
4	chr2:172296199..172299351-chr2:172302148..172304062,3	K562	blood:
5	chr2:172287467..172293160-chr2:172293206..172300397,21	K562	blood:

Variant related genes	Relation type
ENSG00000115827	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000233762	Chromatin interaction
ENSG00000071967	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10490604	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10930476	0.86[ASN][1000 genomes]
rs13384194	0.89[ASN][1000 genomes]
rs1476111	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17221346	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28420126	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28742013	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4496302	0.80[AMR][1000 genomes]
rs4667689	0.83[ASN][1000 genomes]
rs4668385	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57099324	0.81[ASN][1000 genomes]
rs58182652	0.90[ASN][1000 genomes]
rs58267868	0.90[ASN][1000 genomes]
rs62183464	0.80[EUR][1000 genomes]
rs62183492	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62183504	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62183537	0.90[ASN][1000 genomes]
rs62183540	0.89[ASN][1000 genomes]
rs6433291	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433292	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6713612	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6718740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6743290	0.80[ASN][1000 genomes]
rs6751956	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572334	0.81[ASN][1000 genomes]
rs7594714	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7600478	0.89[ASN][1000 genomes]
rs7606658	0.80[ASN][1000 genomes]
rs9789380	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv3349868	chr2:172276494-172302401	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172291000-172319800	Weak transcription	Stomach Mucosa	stomach
2	chr2:172291400-172297800	Weak transcription	Esophagus	oesophagus
3	chr2:172291400-172297800	Weak transcription	Gastric	stomach
4	chr2:172291600-172297800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:172291600-172304000	Weak transcription	Pancreas	Pancrea
6	chr2:172291600-172305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:172291600-172311800	Weak transcription	Fetal Brain Male	brain
8	chr2:172291800-172297800	Weak transcription	HSMMtube	muscle
9	chr2:172291800-172300000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:172291800-172306400	Weak transcription	Psoas Muscle	Psoas
11	chr2:172291800-172338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:172292000-172297200	Weak transcription	NHLF	lung
13	chr2:172292000-172304400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:172292000-172312800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:172292000-172341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:172292200-172297400	Weak transcription	Hela-S3	cervix
17	chr2:172292400-172298600	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr2:172292400-172299400	Strong transcription	Fetal Muscle Leg	muscle
19	chr2:172292400-172301200	Strong transcription	Placenta	Placenta
20	chr2:172292400-172301800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:172292600-172297000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:172292600-172297200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:172292600-172297400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:172292600-172298000	Strong transcription	Primary B cells from cord blood	blood
25	chr2:172292600-172298600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr2:172292600-172301200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr2:172292600-172301400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:172292600-172302000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:172292600-172302600	Strong transcription	Liver	Liver
30	chr2:172292600-172302800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:172292600-172307200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:172292600-172311600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:172292600-172312000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr2:172292600-172317600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:172292600-172320400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:172292800-172298400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:172292800-172300200	Strong transcription	K562	blood
38	chr2:172292800-172301400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:172292800-172301600	Strong transcription	Adipose Nuclei	Adipose
40	chr2:172292800-172302600	Strong transcription	Fetal Thymus	thymus
41	chr2:172292800-172303000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr2:172293000-172297000	Strong transcription	A549	lung
43	chr2:172293000-172297400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:172293000-172298400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:172293000-172298600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr2:172293000-172299400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:172293000-172302000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:172293000-172302600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:172293000-172318600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:172293200-172297200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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