Variant report

Variant	rs13380400
Chromosome Location	chr15:55490518-55490519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr15:55487285-55490596	SK-N-SH	brain:	n/a	n/a
2	KAP1	chr15:55490216-55492297	K562	blood:	n/a	n/a
3	HCFC1	chr15:55488000-55490587	Hela-S3	cervix:	n/a	n/a
4	SETDB1	chr15:55490329-55491659	K562	blood:	n/a	n/a
5	POLR2A	chr15:55490412-55491293	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55489042..55491644-chr15:55640711..55643190,2	K562	blood:
2	chr15:55489860..55492561-chr15:55500870..55502505,2	K562	blood:
3	chr15:55488451..55490602-chr15:55640573..55642962,2	MCF-7	breast:
4	chr15:55485508..55492313-chr15:55579801..55583590,12	K562	blood:
5	chr15:55490157..55491866-chr15:55610487..55612972,2	MCF-7	breast:
6	chr15:54266407..54270072-chr15:55486535..55491034,4	MCF-7	breast:

No data

Variant related genes	Relation type
RSL24D1	TF binding region
ENSG00000259669	Chromatin interaction
ENSG00000225973	Chromatin interaction
ENSG00000260916	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000069943	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10162819	0.84[ASN][1000 genomes]
rs10162843	0.84[ASN][1000 genomes]
rs1050931	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10518804	0.93[ASN][1000 genomes]
rs1061821	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1061822	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061823	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061824	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061870	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061873	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061874	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1061875	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852763	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855907	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855973	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855978	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11856010	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857087	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12385963	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13733	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16976094	0.83[ASN][1000 genomes]
rs16976116	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16976149	0.84[ASN][1000 genomes]
rs17238171	0.83[ASN][1000 genomes]
rs28433503	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28449712	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28489312	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28499113	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28508034	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28522816	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28526269	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28530662	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28535372	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28541469	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28558576	0.83[ASN][1000 genomes]
rs28562431	0.84[ASN][1000 genomes]
rs28564077	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28589384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28589609	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28590021	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28591259	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28630909	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28636526	0.93[ASN][1000 genomes]
rs28649719	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28673043	0.90[ASN][1000 genomes]
rs28699327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28704109	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706531	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28708989	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28710976	0.92[ASN][1000 genomes]
rs28714578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28784096	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28864456	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28889339	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2899580	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899582	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3179664	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759861	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3759862	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809539	0.89[ASN][1000 genomes]
rs3809540	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4238316	0.83[ASN][1000 genomes]
rs4503734	0.90[ASN][1000 genomes]
rs4545742	0.82[ASN][1000 genomes]
rs56328329	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62020097	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62020114	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62020115	0.84[ASN][1000 genomes]
rs6493768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493769	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493771	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7165491	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7168472	0.92[ASN][1000 genomes]
rs7168737	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172108	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172289	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176676	0.90[ASN][1000 genomes]
rs7179365	0.84[ASN][1000 genomes]
rs7180594	0.84[ASN][1000 genomes]
rs73409851	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73409853	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8027098	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027256	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028525	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8030981	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8031949	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033588	0.84[ASN][1000 genomes]
rs8034063	0.84[ASN][1000 genomes]
rs8034402	0.92[ASN][1000 genomes]
rs8034853	0.84[ASN][1000 genomes]
rs8034882	0.84[ASN][1000 genomes]
rs8035625	0.92[ASN][1000 genomes]
rs8043029	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9300	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920136	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920165	0.84[ASN][1000 genomes]
rs9920219	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920220	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920737	0.80[EUR][1000 genomes];0.91[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
rs13380400	PIGB	cis	Artery Tibial	GTEx
rs13380400	RAB27A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55485600-55490600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:55488000-55490600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr15:55489600-55497600	Weak transcription	Gastric	stomach
4	chr15:55489600-55504000	Weak transcription	Spleen	Spleen
5	chr15:55489600-55513200	Weak transcription	Lung	lung
6	chr15:55489800-55490600	Flanking Active TSS	Dnd41	blood
7	chr15:55489800-55499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:55489800-55503400	Weak transcription	Pancreas	Pancrea
9	chr15:55489800-55540200	Weak transcription	Esophagus	oesophagus
10	chr15:55490000-55490600	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr15:55490000-55490600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr15:55490000-55490600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr15:55490000-55490800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:55490000-55491000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr15:55490000-55493800	Weak transcription	Stomach Mucosa	stomach
16	chr15:55490000-55496000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:55490000-55496400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:55490000-55496600	Weak transcription	Liver	Liver
19	chr15:55490000-55496800	Weak transcription	Placenta	Placenta
20	chr15:55490000-55497400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:55490000-55497400	Weak transcription	Adipose Nuclei	Adipose
22	chr15:55490000-55497600	Weak transcription	Fetal Stomach	stomach
23	chr15:55490000-55501600	Weak transcription	Left Ventricle	heart
24	chr15:55490000-55502000	Weak transcription	Colonic Mucosa	Colon
25	chr15:55490000-55509600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:55490000-55510000	Weak transcription	NHLF	lung
27	chr15:55490000-55513000	Weak transcription	Fetal Intestine Large	intestine
28	chr15:55490000-55513200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:55490000-55513200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:55490000-55513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:55490000-55517200	Weak transcription	Aorta	Aorta
32	chr15:55490000-55529400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:55490000-55562800	Weak transcription	Ovary	ovary
34	chr15:55490200-55490600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr15:55490200-55490600	Enhancers	A549	lung
36	chr15:55490200-55490600	Enhancers	Hela-S3	cervix
37	chr15:55490200-55490600	Enhancers	NHEK	skin
38	chr15:55490200-55491000	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr15:55490200-55491200	Weak transcription	Fetal Heart	heart
40	chr15:55490200-55494200	Weak transcription	HepG2	liver
41	chr15:55490200-55494400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:55490200-55496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:55490200-55496400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:55490200-55496600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:55490200-55496800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:55490200-55497000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:55490200-55497000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr15:55490200-55497000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:55490200-55497200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:55490200-55497200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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