Variant report

Variant	rs1153850
Chromosome Location	chr15:45694983-45694984
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:218)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:218 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:45693792-45695227	GM12878	blood:	n/a	n/a
2	CEBPB	chr15:45694050-45695135	IMR90	lung:	n/a	n/a
3	POLR2A	chr15:45693983-45695356	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:45694204-45695771	GM12878	blood:	n/a	n/a
5	GABPA	chr15:45694316-45695154	GM12878	blood:	n/a	chr15:45694521-45694535 chr15:45694523-45694532 chr15:45694562-45694569 chr15:45694521-45694530 chr15:45694521-45694532
6	YY1	chr15:45694328-45695871	HepG2	liver:	n/a	n/a
7	MAX	chr15:45693878-45695301	ECC-1	luminal epithelium:	n/a	n/a
8	TAF1	chr15:45694183-45695250	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr15:45694009-45695355	GM18526	blood:	n/a	n/a
10	POLR2A	chr15:45694272-45695176	A549	lung:	n/a	n/a
11	POLR2A	chr15:45694924-45695177	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr15:45694917-45695716	ECC-1	luminal epithelium:	n/a	n/a
13	MAZ	chr15:45693871-45695868	K562	blood:	n/a	n/a
14	CTCF	chr15:45694940-45695090	HBMEC	blood vessel:	n/a	n/a
15	POLR2A	chr15:45693764-45695111	K562	blood:	n/a	n/a
16	POLR2A	chr15:45694215-45695179	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:45694160-45695038	MCF-7	breast:	n/a	n/a
18	POLR2A	chr15:45694147-45695015	HCT-116	colon:	n/a	n/a
19	POLR2A	chr15:45693891-45695837	HepG2	liver:	n/a	n/a
20	HMGN3	chr15:45694371-45696019	K562	blood:	n/a	n/a
21	MAX	chr15:45694427-45695347	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr15:45693960-45696081	Hela-S3	cervix:	n/a	n/a
23	MTA3	chr15:45693666-45695134	GM12878	blood:	n/a	n/a
24	E2F6	chr15:45694297-45695251	H1-hESC	embryonic stem cell:	n/a	chr15:45694522-45694531
25	RCOR1	chr15:45693605-45695236	IMR90	lung:	n/a	n/a
26	POLR2A	chr15:45694834-45695218	GM12891	blood:	n/a	n/a
27	CREB1	chr15:45694869-45695126	A549	lung:	n/a	n/a
28	MAX	chr15:45693906-45695241	GM12878	blood:	n/a	n/a
29	RCOR1	chr15:45693888-45696299	Hela-S3	cervix:	n/a	n/a
30	UBTF	chr15:45694004-45696027	K562	blood:	n/a	n/a
31	CTCF	chr15:45694980-45695130	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr15:45694160-45695957	K562	blood:	n/a	n/a
33	ZNF143	chr15:45694007-45695123	GM12878	blood:	n/a	n/a
34	TAF1	chr15:45694059-45695132	Hela-S3	cervix:	n/a	n/a
35	CTBP2	chr15:45694383-45695649	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr15:45694239-45695368	A549	lung:	n/a	n/a
37	USF1	chr15:45694937-45695240	H1-hESC	embryonic stem cell:	n/a	chr15:45695065-45695076
38	POLR2A	chr15:45694156-45695168	GM15510	blood:	n/a	n/a
39	POLR2A	chr15:45694076-45696112	Hela-S3	cervix:	n/a	n/a
40	MAX	chr15:45694893-45695176	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr15:45693954-45695030	A549	lung:	n/a	n/a
42	TAF1	chr15:45694183-45695801	HepG2	liver:	n/a	n/a
43	HCFC1	chr15:45693468-45696451	Hela-S3	cervix:	n/a	n/a
44	YY1	chr15:45694176-45695298	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:45693853-45695894	Raji	blood:	n/a	n/a
46	CTCF	chr15:45694840-45695110	GM12873	blood:	n/a	n/a
47	STAT5A	chr15:45693692-45695160	GM12878	blood:	n/a	chr15:45693747-45693759
48	GABPA	chr15:45694174-45695019	HL-60	blood:	n/a	chr15:45694521-45694535 chr15:45694523-45694532 chr15:45694562-45694569 chr15:45694521-45694530 chr15:45694521-45694532
49	MYC	chr15:45694353-45696113	A549	lung:	n/a	n/a
50	POLR2A	chr15:45693786-45695803	GM19099	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:45471561..45475350-chr15:45693833..45697444,3	MCF-7	breast:
2	chr12:44199711..44200638-chr15:45694089..45695040,2	NB4	blood:
3	chr15:45443245..45445612-chr15:45693741..45696247,2	K562	blood:
4	chr15:45491292..45493253-chr15:45693461..45696308,4	K562	blood:
5	chr15:45694437..45696115-chr8:101962201..101965108,2	MCF-7	breast:
6	chr15:45459071..45462844-chr15:45693635..45696532,4	K562	blood:
7	chr15:45693902..45696245-chr15:45709725..45712520,2	K562	blood:
8	chr15:45570708..45573284-chr15:45693152..45695793,2	MCF-7	breast:
9	chr15:45458882..45460694-chr15:45692968..45695992,3	MCF-7	breast:
10	chr15:45693513..45696404-chr15:45876472..45881031,4	MCF-7	breast:
11	chr15:45489573..45492565-chr15:45693942..45696435,3	MCF-7	breast:
12	chr15:44955315..44955922-chr15:45694323..45695000,2	NB4	blood:
13	chr15:45693986..45696362-chr15:45736299..45740535,4	MCF-7	breast:
14	chr15:45497455..45498005-chr15:45694577..45695511,2	K562	blood:
15	chr15:45490733..45493253-chr15:45692978..45696308,3	K562	blood:
16	chr15:45694563..45696942-chr15:45878361..45881039,2	K562	blood:
17	chr15:45693917..45694984-chr6:160210614..160211334,3	Hela-S3	cervix:
18	chr15:45459427..45462384-chr15:45693635..45696116,3	K562	blood:
19	chr15:45693029..45695760-chr15:45741637..45746369,4	MCF-7	breast:
20	chr15:45694529..45695513-chr17:27046875..27047495,2	Hela-S3	cervix:
21	chr15:45694198..45696265-chr15:45878361..45881505,3	K562	blood:
22	chr15:45694962..45695650-chr19:1261794..1262312,2	Hela-S3	cervix:
23	chr15:45694923..45696490-chr15:45729274..45731615,2	K562	blood:
24	chr15:45693316..45695933-chr15:45878534..45881095,2	MCF-7	breast:
25	chr15:45493253..45495607-chr15:45694426..45696533,2	K562	blood:
26	chr15:45694376..45695055-chr3:128444885..128445547,3	Hela-S3	cervix:
27	chr1:40506186..40507999-chr15:45694737..45696787,2	MCF-7	breast:
28	chr15:45694469..45695046-chr5:43483496..43484152,3	Hela-S3	cervix:

No data

Variant related genes	Relation type
SPATA5L1	TF binding region
GATM	TF binding region
ENSG00000138606	Chromatin interaction
ENSG00000259354	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000104164	Chromatin interaction
ENSG00000075785	Chromatin interaction
ENSG00000198242	Chromatin interaction
ENSG00000151239	Chromatin interaction
ENSG00000259539	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000260170	Chromatin interaction
ENSG00000112110	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000137857	Chromatin interaction
ENSG00000120438	Chromatin interaction
ENSG00000259520	Chromatin interaction
ENSG00000099622	Chromatin interaction
ENSG00000259932	Chromatin interaction
ENSG00000259519	Chromatin interaction
ENSG00000252285	Chromatin interaction
ENSG00000131236	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1055395	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070455	1.00[EUR][1000 genomes]
rs1145072	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145073	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145075	0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1145082	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145092	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145094	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1145099	0.86[YRI][hapmap]
rs1153848	0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1153851	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153856	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153859	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1346265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1403319	1.00[EUR][1000 genomes]
rs1464558	1.00[EUR][1000 genomes]
rs1706775	1.00[EUR][1000 genomes]
rs1706782	1.00[EUR][1000 genomes]
rs1706783	1.00[EUR][1000 genomes]
rs1706784	1.00[EUR][1000 genomes]
rs1706786	1.00[EUR][1000 genomes]
rs1706788	1.00[EUR][1000 genomes]
rs1706789	1.00[EUR][1000 genomes]
rs1706790	1.00[EUR][1000 genomes]
rs1706794	1.00[EUR][1000 genomes]
rs1706795	1.00[EUR][1000 genomes]
rs1706796	1.00[EUR][1000 genomes]
rs1706797	1.00[EUR][1000 genomes]
rs1706800	0.80[YRI][hapmap]
rs1706801	0.90[YRI][hapmap]
rs1719242	1.00[EUR][1000 genomes]
rs1719249	1.00[EUR][1000 genomes]
rs1834686	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1874318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2217121	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2413765	0.83[AMR][1000 genomes]
rs2433603	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433604	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433605	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433609	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2433610	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453547	0.83[AMR][1000 genomes]
rs2461704	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467852	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467855	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467857	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2467859	0.83[AMR][1000 genomes]
rs2486271	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486273	0.82[AFR][1000 genomes]
rs2486287	0.81[YRI][hapmap]
rs2486289	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486290	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2668740	1.00[EUR][1000 genomes]
rs2687513	1.00[EUR][1000 genomes]
rs57553327	1.00[EUR][1000 genomes]
rs7163395	1.00[EUR][1000 genomes]
rs7163751	1.00[EUR][1000 genomes]
rs7164252	1.00[EUR][1000 genomes]
rs7169175	1.00[EUR][1000 genomes]
rs7173541	1.00[EUR][1000 genomes]
rs7179186	1.00[EUR][1000 genomes]
rs7179844	1.00[EUR][1000 genomes]
rs74009622	1.00[EUR][1000 genomes]
rs8024550	0.83[AMR][1000 genomes]
rs8028061	1.00[EUR][1000 genomes]
rs8033329	1.00[EUR][1000 genomes]
rs8040380	1.00[EUR][1000 genomes]
rs9806260	1.00[EUR][1000 genomes]
rs9972564	1.00[EUR][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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1153850	SPATA5L1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45693200-45695000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:45693200-45696000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:45693200-45696400	Active TSS	Aorta	Aorta
4	chr15:45693200-45696800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:45693400-45695600	Active TSS	Brain Anterior Caudate	brain
6	chr15:45693400-45696000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr15:45693400-45696000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr15:45693400-45696200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr15:45693400-45696600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr15:45693400-45697000	Active TSS	Fetal Intestine Large	intestine
11	chr15:45693400-45697600	Active TSS	GM12878-XiMat	blood
12	chr15:45693600-45695400	Active TSS	Right Ventricle	heart
13	chr15:45693600-45695600	Active TSS	Fetal Thymus	thymus
14	chr15:45693600-45695800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:45693600-45695800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:45693600-45695800	Active TSS	Fetal Brain Male	brain
17	chr15:45693600-45695800	Active TSS	K562	blood
18	chr15:45693600-45696000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr15:45693600-45696000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:45693600-45696000	Active TSS	Muscle Satellite Cultured Cells	--
21	chr15:45693600-45696000	Active TSS	Fetal Intestine Small	intestine
22	chr15:45693600-45696000	Active TSS	Fetal Stomach	stomach
23	chr15:45693600-45696200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:45693600-45696200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:45693600-45696200	Active TSS	NHDF-Ad	bronchial
26	chr15:45693600-45696200	Active TSS	NHLF	lung
27	chr15:45693600-45696400	Active TSS	A549	lung
28	chr15:45693600-45696600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr15:45693600-45696600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:45693600-45696600	Active TSS	Psoas Muscle	Psoas
31	chr15:45693600-45697000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr15:45693600-45697200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:45693800-45695000	Active TSS	Stomach Smooth Muscle	stomach
34	chr15:45693800-45695400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:45693800-45695600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:45693800-45695600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:45693800-45695600	Active TSS	Placenta	Placenta
38	chr15:45693800-45695800	Active TSS	Brain Substantia Nigra	brain
39	chr15:45693800-45695800	Active TSS	Fetal Muscle Leg	muscle
40	chr15:45693800-45695800	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr15:45693800-45696000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:45693800-45696000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr15:45693800-45696000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:45693800-45696000	Active TSS	Colon Smooth Muscle	Colon
45	chr15:45693800-45696000	Active TSS	Esophagus	oesophagus
46	chr15:45693800-45696000	Active TSS	Gastric	stomach
47	chr15:45693800-45696000	Active TSS	Pancreas	Pancrea
48	chr15:45693800-45696000	Active TSS	Stomach Mucosa	stomach
49	chr15:45693800-45696000	Active TSS	NHEK	skin
50	chr15:45693800-45696200	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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