Variant report

Variant	rs7165054
Chromosome Location	chr15:40857883-40857884
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr15:40856508-40858049	K562	blood:	n/a	n/a
2	MAZ	chr15:40856423-40857893	IMR90	lung:	n/a	chr15:40857402-40857413 chr15:40857403-40857412
3	FOS	chr15:40857756-40858026	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr15:40857173-40857925	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr15:40856644-40857963	K562	blood:	n/a	chr15:40857402-40857413 chr15:40857403-40857412
6	POLR2A	chr15:40856582-40857954	PFSK-1	brain:	n/a	n/a
7	RFX5	chr15:40856281-40857887	SK-N-SH	brain:	n/a	chr15:40857383-40857397 chr15:40857247-40857260
8	MAX	chr15:40856771-40857928	Hela-S3	cervix:	n/a	chr15:40857402-40857413 chr15:40857403-40857412
9	FOS	chr15:40857768-40857966	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr15:40856696-40857883	K562	blood:	n/a	chr15:40857402-40857413 chr15:40857403-40857412
11	FOSL1	chr15:40857668-40858099	K562	blood:	n/a	n/a
12	POLR2A	chr15:40856628-40857920	Hela-S3	cervix:	n/a	n/a
13	FOSL2	chr15:40857142-40858076	HepG2	liver:	n/a	n/a
14	JUND	chr15:40856741-40858043	K562	blood:	n/a	chr15:40857869-40857880
15	GTF3C2	chr15:40856838-40858354	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr15:40857838-40858010	Hela-S3	cervix:	n/a	n/a
17	MAX	chr15:40856601-40857892	Hela-S3	cervix:	n/a	chr15:40857402-40857413 chr15:40857403-40857412
18	USF1	chr15:40856926-40857915	HCT-116	colon:	n/a	chr15:40857403-40857412 chr15:40857403-40857412 chr15:40857397-40857418 chr15:40857404-40857413 chr15:40857402-40857411
19	JUND	chr15:40857778-40858028	HepG2	liver:	n/a	chr15:40857869-40857880
20	MXI1	chr15:40856248-40858053	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40856304..40858832-chr15:40886132..40888060,2	K562	blood:
2	chr15:40857525..40859323-chr15:40878424..40880579,2	K562	blood:
3	chr15:40857188..40857959-chr3:38496163..38496835,2	Hela-S3	cervix:
4	chr15:40855657..40859262-chr15:40860971..40863634,5	MCF-7	breast:
5	chr15:40856363..40858923-chr15:41165345..41167356,2	K562	blood:

Variant related genes	Relation type
RPUSD2	TF binding region
C15orf57	TF binding region
ENSG00000104140	Chromatin interaction
ENSG00000166133	Chromatin interaction
ENSG00000137812	Chromatin interaction
ENSG00000229589	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1051482	0.83[EUR][1000 genomes]
rs10851396	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11070279	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070280	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852479	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11855517	0.81[EUR][1000 genomes]
rs11857247	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148185	0.86[EUR][1000 genomes]
rs12899408	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906755	0.85[EUR][1000 genomes]
rs12907448	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12907984	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12908114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908443	0.87[EUR][1000 genomes]
rs12908867	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12914501	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915563	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12916323	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1453183	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17746659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747399	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2123534	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28798094	0.81[EUR][1000 genomes]
rs3213999	0.80[EUR][1000 genomes]
rs34303240	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34750756	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35030447	0.81[EUR][1000 genomes]
rs35884042	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36094699	0.81[EUR][1000 genomes]
rs3743146	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803353	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4457966	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55954396	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56384845	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61048252	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62018030	0.81[EUR][1000 genomes]
rs62018046	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62018048	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62018051	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62019866	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62019883	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62019934	0.80[EUR][1000 genomes]
rs7162749	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7164385	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7181909	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72733469	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs731640	0.81[EUR][1000 genomes]
rs8025458	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8028910	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8036938	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8038396	0.85[EUR][1000 genomes]
rs8042733	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806410	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs7165054	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs7165054	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs7165054	C15orf57	cis	Nerve Tibial	GTEx
rs7165054	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs7165054	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs7165054	C15orf57	cis	Artery Tibial	GTEx
rs7165054	ZFYVE19	cis	multi-tissue	Pritchard
rs7165054	RP11-111A22.1	cis	Artery Tibial	GTEx
rs7165054	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs7165054	C15orf57	cis	Esophagus Muscularis	GTEx
rs7165054	C15orf57	cis	Muscle Skeletal	GTEx
rs7165054	C15orf57	cis	Stomach	GTEx
rs7165054	CCDC32	cis	multi-tissue	Pritchard
rs7165054	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs7165054	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs7165054	RP11-111A22.1	cis	lung	GTEx
rs7165054	C15orf57	cis	Adipose Subcutaneous	GTEx
rs7165054	RP11-111A22.1	cis	Artery Aorta	GTEx
rs7165054	C15orf57	cis	Artery Aorta	GTEx
rs7165054	C15orf57	cis	Esophagus Mucosa	GTEx
rs7165054	C15orf57	cis	lung	GTEx
rs7165054	RP11-111A22.1	cis	Stomach	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40855200-40858000	Active TSS	GM12878-XiMat	blood
2	chr15:40856400-40858000	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr15:40856400-40858000	Active TSS	A549	lung
4	chr15:40856600-40858000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:40856600-40858000	Active TSS	Brain Hippocampus Middle	brain
6	chr15:40856600-40858000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr15:40856600-40858000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:40856600-40858000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr15:40856600-40858400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr15:40856800-40858000	Active TSS	Brain Anterior Caudate	brain
11	chr15:40856800-40858000	Active TSS	Thymus	Thymus
12	chr15:40857200-40859200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:40857200-40861200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:40857400-40858000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr15:40857400-40858000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr15:40857400-40858000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:40857400-40858000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr15:40857400-40858000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:40857400-40858000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:40857400-40858000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:40857400-40858000	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr15:40857400-40858000	Flanking Active TSS	Dnd41	blood
23	chr15:40857400-40860800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:40857600-40858000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr15:40857600-40858000	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr15:40857600-40858000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr15:40857600-40858000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr15:40857600-40858000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr15:40857600-40858000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr15:40857600-40858000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:40857600-40858000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:40857600-40858000	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr15:40857600-40858000	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr15:40857600-40858000	Enhancers	Lung	lung
35	chr15:40857600-40858000	Enhancers	Pancreas	Pancrea
36	chr15:40857600-40858000	Enhancers	Placenta Amnion	Placenta Amnion
37	chr15:40857600-40858000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr15:40857600-40858000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr15:40857600-40858200	Flanking Active TSS	Hela-S3	cervix
40	chr15:40857600-40858200	Flanking Active TSS	HepG2	liver
41	chr15:40857600-40860800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:40857800-40858000	Enhancers	H1 Cell Line	embryonic stem cell
43	chr15:40857800-40858000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:40857800-40858000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr15:40857800-40858000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:40857800-40858000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:40857800-40858000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr15:40857800-40858000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr15:40857800-40858000	Enhancers	Primary T cells from cord blood	blood
50	chr15:40857800-40858000	Enhancers	Primary hematopoietic stem cells	blood

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