Variant report

Variant	rs62020097
Chromosome Location	chr15:55491007-55491008
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr15:55490879-55491276	K562	blood:	n/a	n/a
2	SETDB1	chr15:55490650-55491551	U2OS	brain:	n/a	n/a
3	CBX3	chr15:55490666-55491337	K562	blood:	n/a	n/a
4	KAP1	chr15:55490216-55492297	K562	blood:	n/a	n/a
5	SETDB1	chr15:55490329-55491659	K562	blood:	n/a	n/a
6	POLR2A	chr15:55490412-55491293	K562	blood:	n/a	n/a
7	RCOR1	chr15:55490877-55491173	K562	blood:	n/a	n/a
8	SETDB1	chr15:55490851-55491319	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55468513..55470349-chr15:55490736..55492904,2	K562	blood:
2	chr15:55489042..55491644-chr15:55640711..55643190,2	K562	blood:
3	chr15:55487872..55490645-chr15:55490710..55492637,2	K562	blood:
4	chr15:55489860..55492561-chr15:55500870..55502505,2	K562	blood:
5	chr15:55485508..55492313-chr15:55579801..55583590,12	K562	blood:
6	chr15:55490157..55491866-chr15:55610487..55612972,2	MCF-7	breast:
7	chr15:54266407..54270072-chr15:55486535..55491034,4	MCF-7	breast:

No data

Variant related genes	Relation type
RSL24D1	TF binding region
ENSG00000259669	Chromatin interaction
ENSG00000137876	Chromatin interaction
ENSG00000225973	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000069943	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1050931	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1061821	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1061822	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1061823	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1061824	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1061870	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1061873	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1061874	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1061875	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11852763	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11855907	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11855973	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11855978	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11856010	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12385963	0.85[AFR][1000 genomes]
rs13380400	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13733	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs28433503	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28449712	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28489312	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28508034	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28522816	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28526269	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28530662	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28535372	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28541469	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28564077	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28589384	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28590021	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28591259	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28630909	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28649719	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28699327	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28704109	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28708989	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28714578	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899580	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899581	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899582	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3179664	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3759862	0.85[AFR][1000 genomes]
rs3809540	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62020114	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493768	0.85[AFR][1000 genomes]
rs6493769	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7165491	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7168737	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7172108	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7172289	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73409853	0.80[EUR][1000 genomes]
rs8027098	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8027256	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8028525	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8030981	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8031949	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9300	0.86[AFR][1000 genomes];0.82[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62020097	RAB27A	Cis_1M	lymphoblastoid	RTeQTL
rs62020097	PIGB	cis	Artery Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55489600-55497600	Weak transcription	Gastric	stomach
2	chr15:55489600-55504000	Weak transcription	Spleen	Spleen
3	chr15:55489600-55513200	Weak transcription	Lung	lung
4	chr15:55489800-55499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:55489800-55503400	Weak transcription	Pancreas	Pancrea
6	chr15:55489800-55540200	Weak transcription	Esophagus	oesophagus
7	chr15:55490000-55493800	Weak transcription	Stomach Mucosa	stomach
8	chr15:55490000-55496000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:55490000-55496400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:55490000-55496600	Weak transcription	Liver	Liver
11	chr15:55490000-55496800	Weak transcription	Placenta	Placenta
12	chr15:55490000-55497400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:55490000-55497400	Weak transcription	Adipose Nuclei	Adipose
14	chr15:55490000-55497600	Weak transcription	Fetal Stomach	stomach
15	chr15:55490000-55501600	Weak transcription	Left Ventricle	heart
16	chr15:55490000-55502000	Weak transcription	Colonic Mucosa	Colon
17	chr15:55490000-55509600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:55490000-55510000	Weak transcription	NHLF	lung
19	chr15:55490000-55513000	Weak transcription	Fetal Intestine Large	intestine
20	chr15:55490000-55513200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:55490000-55513200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:55490000-55513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:55490000-55517200	Weak transcription	Aorta	Aorta
24	chr15:55490000-55529400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:55490000-55562800	Weak transcription	Ovary	ovary
26	chr15:55490200-55491200	Weak transcription	Fetal Heart	heart
27	chr15:55490200-55494200	Weak transcription	HepG2	liver
28	chr15:55490200-55494400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:55490200-55496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:55490200-55496400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:55490200-55496600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:55490200-55496800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:55490200-55497000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:55490200-55497000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:55490200-55497000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:55490200-55497200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:55490200-55497200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:55490200-55499400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:55490200-55510000	Weak transcription	Fetal Kidney	kidney
40	chr15:55490200-55510200	Weak transcription	Fetal Lung	lung
41	chr15:55490200-55511400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:55490200-55511400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr15:55490200-55511400	Weak transcription	Osteobl	bone
44	chr15:55490200-55513200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:55490200-55513800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:55490200-55514000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr15:55490400-55493800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:55490400-55493800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr15:55490400-55495000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr15:55490400-55496600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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