Variant report

Variant	rs8025447
Chromosome Location	chr15:75192222-75192223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75192144-75193185	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:75187739-75194836	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr15:75191960-75193280	HCT-116	colon:	n/a	n/a
4	POLR2A	chr15:75191966-75192412	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr15:75191924-75193436	U87	brain:	n/a	n/a
6	POLR2A	chr15:75192141-75192592	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr15:75191083-75193522	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:75192196-75193527	GM12891	blood:	n/a	n/a
9	POLR2A	chr15:75191618-75193452	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:75188926-75194641	U87	brain:	n/a	n/a
11	POLR2A	chr15:75191051-75193164	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr15:75192137-75193430	HepG2	liver:	n/a	n/a
13	POLR2A	chr15:75192043-75193441	HCT-116	colon:	n/a	n/a
14	POLR2A	chr15:75192215-75193282	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr15:75188926-75193508	U87	brain:	n/a	n/a
16	POLR2A	chr15:75191042-75193090	GM12892	blood:	n/a	n/a
17	POLR2A	chr15:75187473-75194577	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr15:75192192-75193350	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr15:75187279-75194196	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:75191166-75193177	K562	blood:	n/a	n/a
21	POLR2A	chr15:75191137-75195522	K562	blood:	n/a	n/a
22	POLR2A	chr15:75192145-75193436	U87	brain:	n/a	n/a
23	POLR2A	chr15:75187680-75194520	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr15:75192206-75192230	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr15:75191144-75194333	K562	blood:	n/a	n/a
26	POLR2A	chr15:75188556-75193697	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr15:75192175-75192239	MCF-7	breast:	n/a	n/a
28	POLR2A	chr15:75188034-75193326	PFSK-1	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
2	chr15:75163746..75165751-chr15:75191304..75195509,4	K562	blood:
3	chr15:75132595..75137581-chr15:75190842..75194074,4	K562	blood:
4	chr15:75161914..75167776-chr15:75191644..75199761,13	MCF-7	breast:
5	chr15:75191256..75201000-chr15:75228549..75233626,13	K562	blood:
6	chr15:75144129..75146019-chr15:75191068..75193901,2	MCF-7	breast:
7	chr15:75181107..75185393-chr15:75190667..75200295,16	MCF-7	breast:
8	chr15:75134794..75137581-chr15:75190842..75193156,3	K562	blood:
9	chr15:75091765..75094357-chr15:75191183..75194158,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260824	TF binding region
ENSG00000103653	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11072511	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072512	0.98[EUR][1000 genomes]
rs11072513	0.84[EUR][1000 genomes]
rs11072514	0.87[EUR][1000 genomes]
rs1127796	1.00[EUR][1000 genomes]
rs1130741	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133322	0.96[EUR][1000 genomes]
rs1133323	0.88[EUR][1000 genomes]
rs11630918	0.83[EUR][1000 genomes]
rs11633472	0.89[EUR][1000 genomes]
rs11638130	0.88[EUR][1000 genomes]
rs11639413	0.81[EUR][1000 genomes]
rs11854704	0.92[EUR][1000 genomes]
rs11856413	0.90[EUR][1000 genomes]
rs11857695	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12439641	0.82[AFR][1000 genomes]
rs12441499	0.84[AFR][1000 genomes]
rs12898539	0.89[EUR][1000 genomes]
rs12899430	0.89[EUR][1000 genomes]
rs12899787	0.94[EUR][1000 genomes]
rs12900662	0.91[EUR][1000 genomes]
rs12901190	0.86[EUR][1000 genomes]
rs12902515	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12903205	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12903370	0.87[EUR][1000 genomes]
rs12904326	0.86[EUR][1000 genomes]
rs12904897	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12907898	0.97[EUR][1000 genomes]
rs12908365	0.95[EUR][1000 genomes]
rs12909335	0.88[EUR][1000 genomes]
rs12911254	0.85[EUR][1000 genomes]
rs12912839	0.87[EUR][1000 genomes]
rs12913293	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12914217	0.86[EUR][1000 genomes]
rs2044157	0.84[EUR][1000 genomes]
rs2415251	0.81[EUR][1000 genomes]
rs3935818	0.85[AFR][1000 genomes]
rs4643278	0.92[EUR][1000 genomes]
rs4886608	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4886632	0.95[EUR][1000 genomes]
rs4886636	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886639	0.89[EUR][1000 genomes]
rs4886640	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs56671860	0.84[AFR][1000 genomes]
rs59945415	0.95[EUR][1000 genomes]
rs60494786	0.84[AFR][1000 genomes]
rs62029167	0.95[EUR][1000 genomes]
rs6495128	0.83[ASN][1000 genomes]
rs6495129	0.83[ASN][1000 genomes]
rs7179093	0.85[AFR][1000 genomes]
rs729263	0.84[AFR][1000 genomes]
rs7495664	0.88[EUR][1000 genomes]
rs7495739	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7497026	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7497393	0.86[EUR][1000 genomes]
rs8032473	0.80[AFR][1000 genomes]
rs9672491	0.80[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8025447	ULK3	cis	Whole Blood	GTEx
rs8025447	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs8025447	SCAMP2	cis	Whole Blood	GTEx
rs8025447	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs8025447	SCAMP5	cis	Artery Tibial	GTEx
rs8025447	SCAMP2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75183200-75192400	Weak transcription	HUVEC	blood vessel
2	chr15:75183200-75197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:75183600-75193800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:75183600-75193800	Strong transcription	Fetal Stomach	stomach
5	chr15:75184000-75195400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:75184200-75192400	Weak transcription	Fetal Brain Male	brain
7	chr15:75184200-75196600	Weak transcription	Small Intestine	intestine
8	chr15:75185000-75193800	Strong transcription	Fetal Intestine Small	intestine
9	chr15:75185000-75194800	Weak transcription	Right Atrium	heart
10	chr15:75185200-75193800	Strong transcription	Fetal Intestine Large	intestine
11	chr15:75185200-75197000	Weak transcription	Fetal Heart	heart
12	chr15:75185800-75192600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:75186200-75192400	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:75186200-75193600	Weak transcription	Stomach Mucosa	stomach
15	chr15:75186800-75195800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:75187000-75192400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:75187200-75193400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:75187200-75193600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:75187400-75193600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr15:75187600-75193600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:75187600-75193800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:75187600-75197200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:75187800-75193600	Strong transcription	Primary T cells from cord blood	blood
24	chr15:75187800-75193800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr15:75187800-75193800	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:75187800-75194000	Strong transcription	A549	lung
27	chr15:75187800-75196600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:75187800-75196800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:75187800-75197400	Strong transcription	Fetal Thymus	thymus
30	chr15:75188000-75192800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:75188000-75193400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:75188000-75193600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:75188000-75193600	Strong transcription	Liver	Liver
34	chr15:75188000-75193800	Strong transcription	Brain Hippocampus Middle	brain
35	chr15:75188000-75193800	Strong transcription	K562	blood
36	chr15:75188000-75196000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:75188000-75196800	Strong transcription	Brain Germinal Matrix	brain
38	chr15:75188000-75197000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:75188000-75197000	Strong transcription	Fetal Brain Female	brain
40	chr15:75188000-75197600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:75188200-75193400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr15:75188200-75193800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:75188200-75193800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:75188200-75193800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr15:75188200-75195000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:75188200-75195600	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr15:75188200-75197400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:75188200-75197400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:75188200-75197600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr15:75188400-75193600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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