Variant report

Variant	rs2899583
Chromosome Location	chr15:55518545-55518546
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55517285..55519190-chr15:55531855..55534772,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16976187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17238192	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17238199	1.00[JPT][hapmap]
rs17238206	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17819024	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17819036	0.81[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	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv1049977	chr15:55502508-55555694	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2899583	RAB27A	Cis_1M	lymphoblastoid	RTeQTL
rs2899583	PIGB	cis	Artery Tibial	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55489800-55540200	Weak transcription	Esophagus	oesophagus
2	chr15:55490000-55529400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:55490000-55562800	Weak transcription	Ovary	ovary
4	chr15:55508600-55522600	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:55509400-55541600	Weak transcription	Small Intestine	intestine
6	chr15:55510400-55522600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:55510400-55525000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:55510400-55528000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:55510600-55523800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:55510800-55521000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:55512800-55541600	Weak transcription	Colonic Mucosa	Colon
12	chr15:55513400-55532400	Weak transcription	Left Ventricle	heart
13	chr15:55514000-55518600	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr15:55514200-55518600	Strong transcription	Stomach Smooth Muscle	stomach
15	chr15:55514200-55521400	Weak transcription	HUVEC	blood vessel
16	chr15:55514200-55522000	Weak transcription	NH-A	brain
17	chr15:55514200-55522200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:55514200-55523000	Weak transcription	NHEK	skin
19	chr15:55514200-55532000	Weak transcription	Lung	lung
20	chr15:55514200-55532600	Weak transcription	Psoas Muscle	Psoas
21	chr15:55514200-55540400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:55514200-55545200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:55514400-55519600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:55514400-55521800	Weak transcription	Fetal Brain Female	brain
25	chr15:55514400-55541200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:55514600-55522400	Weak transcription	HMEC	breast
27	chr15:55514600-55522600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:55514600-55534200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:55514600-55542600	Weak transcription	Hela-S3	cervix
30	chr15:55514600-55543200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:55514800-55522400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:55514800-55532600	Weak transcription	Adipose Nuclei	Adipose
33	chr15:55514800-55539800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:55514800-55560400	Weak transcription	Spleen	Spleen
35	chr15:55515000-55518600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:55515200-55522200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:55515400-55526200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:55515600-55518800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr15:55515600-55520200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:55515600-55520400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:55516000-55524600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
42	chr15:55516000-55559600	Weak transcription	Fetal Stomach	stomach
43	chr15:55516200-55529400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:55516400-55518600	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr15:55517200-55518600	Strong transcription	Placenta	Placenta
46	chr15:55517200-55518800	Strong transcription	Aorta	Aorta
47	chr15:55517200-55519200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:55517200-55520800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:55517600-55518600	Genic enhancers	Monocytes-CD14+_RO01746	blood
50	chr15:55517600-55520000	Weak transcription	Duodenum Mucosa	Duodenum

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