Variant report

Variant	rs1130741
Chromosome Location	chr15:75189930-75189931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:74)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:74 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr15:75189868-75190334	HEK293-T-REx	kidney:	n/a	chr15:75190199-75190220
2	POLR2A	chr15:75187779-75190960	K562	blood:	n/a	n/a
3	POLR2A	chr15:75189238-75190889	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:75187739-75194836	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr15:75189534-75190605	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:75189183-75190865	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:75187943-75190750	HUVEC	blood vessel:	n/a	n/a
8	BCL3	chr15:75189317-75190647	A549	lung:	n/a	n/a
9	POLR2A	chr15:75189520-75190458	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:75189296-75190090	HepG2	liver:	n/a	n/a
11	POLR2A	chr15:75189679-75190904	HCT-116	colon:	n/a	n/a
12	POLR2A	chr15:75188853-75190851	K562	blood:	n/a	n/a
13	POLR2A	chr15:75188189-75190877	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:75189258-75190898	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr15:75189581-75190290	A549	lung:	n/a	n/a
16	POLR2A	chr15:75188363-75190846	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr15:75189157-75190418	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr15:75189676-75190201	ProgFib	skin:	n/a	n/a
19	POLR2A	chr15:75188605-75190890	U87	brain:	n/a	n/a
20	POLR2A	chr15:75189198-75190897	HL-60	blood:	n/a	n/a
21	POLR2A	chr15:75188901-75190853	HCT-116	colon:	n/a	n/a
22	POLR2A	chr15:75188926-75194641	U87	brain:	n/a	n/a
23	POLR2A	chr15:75188855-75190621	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:75187964-75190840	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr15:75189864-75190102	A549	lung:	n/a	n/a
26	POLR2A	chr15:75188787-75190852	K562	blood:	n/a	n/a
27	POLR2A	chr15:75189233-75190417	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:75188309-75190832	GM12891	blood:	n/a	n/a
29	POLR2A	chr15:75188017-75190928	K562	blood:	n/a	n/a
30	POLR2A	chr15:75189803-75190639	GM12891	blood:	n/a	n/a
31	POLR2A	chr15:75189424-75190741	HEK293	kidney:	n/a	n/a
32	POLR2A	chr15:75189260-75190396	HepG2	liver:	n/a	n/a
33	POLR2A	chr15:75189228-75190774	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr15:75188187-75190911	K562	blood:	n/a	n/a
35	POLR2A	chr15:75188926-75193508	U87	brain:	n/a	n/a
36	POLR2A	chr15:75187473-75194577	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr15:75189608-75190313	GM12891	blood:	n/a	n/a
38	POLR2A	chr15:75188765-75190977	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr15:75187941-75190956	HepG2	liver:	n/a	n/a
40	POLR2A	chr15:75188632-75190816	K562	blood:	n/a	n/a
41	POLR2A	chr15:75187279-75194196	HepG2	liver:	n/a	n/a
42	POLR2A	chr15:75188313-75190881	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr15:75188157-75190930	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:75188079-75191035	GM12892	blood:	n/a	n/a
45	POLR2A	chr15:75189217-75190192	GM12878	blood:	n/a	n/a
46	POLR2A	chr15:75188563-75190883	K562	blood:	n/a	n/a
47	POLR2A	chr15:75187680-75194520	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr15:75188612-75190883	MCF-7	breast:	n/a	n/a
49	POLR2A	chr15:75189782-75190116	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr15:75188556-75193697	PANC-1	pancreas:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
2	chr15:75188520..75190057-chr15:75227191..75229624,2	K562	blood:
3	chr15:75165443..75167365-chr15:75189405..75191280,2	MCF-7	breast:

No data

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

Extended variants
information (count: 60 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11072511	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072512	1.00[CEU][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs11072513	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs11072514	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1127796	1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs1133322	0.96[CEU][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs1133323	0.96[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs11630918	0.96[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11633472	1.00[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs11638130	1.00[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs11639413	0.81[EUR][1000 genomes]
rs11854704	0.96[CEU][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs11856413	1.00[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs11857695	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12439641	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs12441499	0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs12487	0.92[CEU][hapmap]
rs12898539	0.89[EUR][1000 genomes]
rs12899430	0.89[EUR][1000 genomes]
rs12899787	0.94[EUR][1000 genomes]
rs12900662	0.92[EUR][1000 genomes]
rs12901190	0.96[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12902515	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12903205	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12903370	0.87[EUR][1000 genomes]
rs12904326	0.87[EUR][1000 genomes]
rs12904897	0.94[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	0.96[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs12911254	0.85[EUR][1000 genomes]
rs12912839	0.87[EUR][1000 genomes]
rs12913293	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12914217	0.86[EUR][1000 genomes]
rs2044157	0.85[EUR][1000 genomes]
rs2415251	0.92[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs3935818	0.95[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs4643278	0.92[EUR][1000 genomes]
rs4886608	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4886632	0.96[EUR][1000 genomes]
rs4886636	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886639	0.88[EUR][1000 genomes]
rs4886640	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56671860	0.86[AFR][1000 genomes]
rs59945415	0.94[EUR][1000 genomes]
rs60494786	0.86[AFR][1000 genomes]
rs62029167	0.95[EUR][1000 genomes]
rs6495122	0.89[CEU][hapmap]
rs6495128	0.83[ASN][1000 genomes]
rs6495129	0.83[ASN][1000 genomes]
rs7179093	0.95[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs729263	0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs7495664	0.88[EUR][1000 genomes]
rs7495739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7497026	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7497393	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs8025447	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8032473	0.82[AFR][1000 genomes]
rs9672491	0.82[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1130741	MPI	cis	multi-tissue	Pritchard
rs1130741	SCAMP2	cis	Whole Blood	GTEx
rs1130741	SCAMP5	cis	Artery Tibial	GTEx
rs1130741	ULK3	cis	parietal	SCAN
rs1130741	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs1130741	MPI	cis	lymphoblastoid	seeQTL
rs1130741	SCAMP2	cis	parietal	SCAN
rs1130741	ZNF572	trans	cerebellum	SCAN
rs1130741	CYP11A1	cis	cerebellum	SCAN
rs1130741	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs1130741	TLE3	cis	cerebellum	SCAN
rs1130741	ETFA	cis	cerebellum	SCAN
rs1130741	ULK3	cis	Whole Blood	GTEx
rs1130741	SCAMP2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75183200-75191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:75183200-75192000	Weak transcription	Fetal Kidney	kidney
3	chr15:75183200-75192400	Weak transcription	HUVEC	blood vessel
4	chr15:75183200-75197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:75183400-75192200	Weak transcription	NH-A	brain
6	chr15:75183600-75193800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:75183600-75193800	Strong transcription	Fetal Stomach	stomach
8	chr15:75184000-75195400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:75184200-75192400	Weak transcription	Fetal Brain Male	brain
10	chr15:75184200-75196600	Weak transcription	Small Intestine	intestine
11	chr15:75185000-75193800	Strong transcription	Fetal Intestine Small	intestine
12	chr15:75185000-75194800	Weak transcription	Right Atrium	heart
13	chr15:75185200-75193800	Strong transcription	Fetal Intestine Large	intestine
14	chr15:75185200-75197000	Weak transcription	Fetal Heart	heart
15	chr15:75185800-75190000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:75185800-75191200	Weak transcription	Aorta	Aorta
17	chr15:75185800-75192600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:75186200-75191200	Weak transcription	Placenta	Placenta
19	chr15:75186200-75191200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:75186200-75191600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:75186200-75192000	Weak transcription	NHDF-Ad	bronchial
22	chr15:75186200-75192400	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:75186200-75193600	Weak transcription	Stomach Mucosa	stomach
24	chr15:75186400-75191600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:75186400-75191800	Weak transcription	Primary B cells from cord blood	blood
26	chr15:75186800-75195800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:75187000-75192400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:75187200-75190000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:75187200-75193400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:75187200-75193600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr15:75187400-75193600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr15:75187600-75193600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:75187600-75193800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:75187600-75197200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:75187800-75193600	Strong transcription	Primary T cells from cord blood	blood
36	chr15:75187800-75193800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr15:75187800-75193800	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:75187800-75194000	Strong transcription	A549	lung
39	chr15:75187800-75196600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:75187800-75196800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:75187800-75197400	Strong transcription	Fetal Thymus	thymus
42	chr15:75188000-75191200	Strong transcription	GM12878-XiMat	blood
43	chr15:75188000-75192800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:75188000-75193400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:75188000-75193600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr15:75188000-75193600	Strong transcription	Liver	Liver
47	chr15:75188000-75193800	Strong transcription	Brain Hippocampus Middle	brain
48	chr15:75188000-75193800	Strong transcription	K562	blood
49	chr15:75188000-75196000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:75188000-75196800	Strong transcription	Brain Germinal Matrix	brain

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