Variant report

Variant	rs654276
Chromosome Location	chr15:44090854-44090855
allele	C/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	POLR2A	chr15:44090434-44094068	GM12891	blood:	n/a	n/a
2	NFIC	chr15:44090736-44091738	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:44090541-44094332	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:44090469-44094494	U87	brain:	n/a	n/a
5	POLR2A	chr15:44090434-44094516	GM12891	blood:	n/a	n/a
6	POLR2A	chr15:44090432-44091899	GM12892	blood:	n/a	n/a
7	MTA3	chr15:44090831-44091925	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:44090364-44093636	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr15:44090553-44091856	GM12891	blood:	n/a	n/a
10	NFATC1	chr15:44090467-44091975	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:44086989-44094589	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr15:44083584-44094591	H1-hESC	embryonic stem cell:	n/a	n/a
13	PML	chr15:44090431-44093563	GM12878	blood:	n/a	chr15:44090782-44090790
14	POLR2A	chr15:44090417-44091858	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr15:44090518-44091449	U87	brain:	n/a	n/a
16	EP300	chr15:44090823-44091500	T-47D	breast:	n/a	n/a
17	POLR2A	chr15:44090372-44093509	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr15:44090795-44091972	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr15:44090470-44093815	MCF10A-Er-Src	breast:	n/a	n/a
20	MTA3	chr15:44090446-44093610	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:44090502-44093448	GM12892	blood:	n/a	n/a
22	POLR2A	chr15:44090585-44094370	K562	blood:	n/a	n/a
23	POLR2A	chr15:44090650-44093627	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:44090496-44094400	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:44090572-44094627	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr15:44090514-44091610	GM12891	blood:	n/a	n/a
27	CHD2	chr15:44090727-44091743	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:44090520-44091810	HL-60	blood:	n/a	n/a
29	POLR2A	chr15:44090541-44094405	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:44090461-44093948	K562	blood:	n/a	n/a
31	ATF2	chr15:44090661-44091448	GM12878	blood:	n/a	n/a
32	POLR2A	chr15:44090533-44094417	HepG2	liver:	n/a	n/a
33	POLR2A	chr15:44090644-44091591	ProgFib	skin:	n/a	n/a
34	IRF1	chr15:44090628-44090937	K562	blood:	n/a	chr15:44090778-44090795 chr15:44090780-44090791 chr15:44090778-44090792 chr15:44090775-44090789 chr15:44090778-44090790 chr15:44090778-44090790 chr15:44090779-44090789 chr15:44090777-44090791 chr15:44090779-44090793 chr15:44090777-44090797
35	RUNX3	chr15:44090806-44092032	GM12878	blood:	n/a	n/a
36	TCF12	chr15:44090830-44091763	MCF-7	breast:	n/a	chr15:44091433-44091440
37	POLR2A	chr15:44090632-44091415	A549	lung:	n/a	n/a
38	POLR2A	chr15:44090515-44094459	GM12891	blood:	n/a	n/a
39	FOXA1	chr15:44090851-44091446	T-47D	breast:	n/a	n/a
40	POLR2A	chr15:44090546-44090911	GM12878	blood:	n/a	n/a
41	STAT5A	chr15:44090436-44093596	GM12878	blood:	n/a	chr15:44093006-44093018 chr15:44090779-44090790
42	CEBPB	chr15:44090822-44091392	MCF-7	breast:	n/a	n/a
43	POLR2A	chr15:44090526-44091871	GM12892	blood:	n/a	n/a
44	POLR2A	chr15:44090411-44091019	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr15:44090566-44091189	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr15:44090479-44090930	K562	blood:	n/a	n/a
47	POLR2A	chr15:44090608-44093434	PBDE	blood:	n/a	n/a
48	POLR2A	chr15:44090467-44091005	HepG2	liver:	n/a	n/a
49	POLR2A	chr15:44090499-44094679	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr15:44090417-44093672	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44082965..44094882-chr15:44108427..44121402,26	K562	blood:
2	chr15:44089939..44094924-chr15:44115270..44119372,7	MCF-7	breast:
3	chr15:44038791..44041212-chr15:44089540..44091517,2	MCF-7	breast:
4	chr15:44089858..44095024-chr15:44113933..44120718,10	MCF-7	breast:
5	chr15:44062113..44074982-chr15:44088756..44097846,29	MCF-7	breast:
6	chr15:44089561..44091456-chr17:44999592..45001929,2	MCF-7	breast:
7	chr15:44090570..44093330-chr8:109259431..109261884,2	MCF-7	breast:
8	chr15:44090279..44093253-chr17:26710935..26712554,2	MCF-7	breast:
9	chr15:44065227..44073214-chr15:44081584..44094479,46	MCF-7	breast:
10	chr10:8094769..8097010-chr15:44089364..44091446,2	MCF-7	breast:

Variant related genes	Relation type
MIR1282	TF binding region
HYPK	TF binding region
SERF2	TF binding region
ENSG00000205771	Chromatin interaction
ENSG00000262633	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000167004	Chromatin interaction
ENSG00000197308	Chromatin interaction
ENSG00000092470	Chromatin interaction
ENSG00000243350	Chromatin interaction
ENSG00000004139	Chromatin interaction
ENSG00000140259	Chromatin interaction
ENSG00000108433	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000104408	Chromatin interaction
ENSG00000107485	Chromatin interaction
ENSG00000261886	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10163069	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs11070411	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs12443084	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap]
rs17727853	0.94[CEU][hapmap]
rs17795279	0.94[CEU][hapmap];0.85[MEX][hapmap]
rs2412821	0.93[CEU][hapmap]
rs2729494	0.94[CEU][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs28410121	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.88[EUR][1000 genomes]
rs2918943	0.87[YRI][hapmap]
rs2918947	0.82[EUR][1000 genomes]
rs2930529	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2930530	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2930531	0.93[ASW][hapmap];0.94[CEU][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2930532	0.86[YRI][hapmap]
rs2930534	0.86[YRI][hapmap]
rs3102448	0.87[EUR][1000 genomes]
rs35822148	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3862143	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs3986209	0.88[EUR][1000 genomes]
rs4644832	0.94[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4923964	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];0.87[YRI][hapmap];0.92[EUR][1000 genomes]
rs494774	0.86[YRI][hapmap]
rs495880	0.85[ASW][hapmap];0.89[CEU][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.86[EUR][1000 genomes]
rs514311	0.89[CEU][hapmap];0.86[YRI][hapmap]
rs528764	0.94[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs541871	0.89[CEU][hapmap];0.87[YRI][hapmap]
rs62018940	0.82[EUR][1000 genomes]
rs6493090	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs678084	0.85[ASW][hapmap];0.94[CEU][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7174260	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs7178230	0.88[EUR][1000 genomes]
rs8030536	0.94[CEU][hapmap];0.85[MEX][hapmap]
rs8038068	0.94[CEU][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	158 gene(s)	inside rSNPs	diseases
9	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs654276	WDR76	cis	parietal	SCAN
rs654276	ZSCAN29	cis	lymphoblastoid	seeQTL
rs654276	TGM5	cis	lymphoblastoid	seeQTL
rs654276	ZSCAN29	cis	multi-tissue	Pritchard
rs654276	STRC	cis	Skin Sun Exposed Lower leg	GTEx
rs654276	TUBGCP4	cis	parietal	SCAN
rs654276	MAPKBP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44086000-44092400	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr15:44086200-44092200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:44086200-44092200	Genic enhancers	Adipose Nuclei	Adipose
4	chr15:44086800-44091000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:44086800-44091400	Strong transcription	Primary hematopoietic stem cells	blood
6	chr15:44086800-44092800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:44087000-44091000	Genic enhancers	Osteobl	bone
8	chr15:44087000-44092000	Strong transcription	Brain Germinal Matrix	brain
9	chr15:44087000-44092000	Strong transcription	Fetal Brain Female	brain
10	chr15:44087000-44092200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
11	chr15:44087200-44091200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:44087200-44092000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:44087200-44092000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:44087400-44092200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:44087600-44091000	Strong transcription	Brain Hippocampus Middle	brain
16	chr15:44087800-44091000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:44087800-44091000	Strong transcription	Thymus	Thymus
18	chr15:44087800-44091200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr15:44087800-44091600	Strong transcription	Brain Cingulate Gyrus	brain
20	chr15:44087800-44092000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:44087800-44092200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:44087800-44092200	Weak transcription	Small Intestine	intestine
23	chr15:44087800-44092400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:44088000-44091000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr15:44088000-44091200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr15:44088000-44091200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:44088000-44091600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:44088000-44091600	Strong transcription	Dnd41	blood
29	chr15:44088000-44092000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
30	chr15:44088000-44092200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:44088200-44091200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:44088200-44091800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:44088200-44092000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:44088400-44092000	Strong transcription	Primary T cells from cord blood	blood
35	chr15:44088400-44092200	Strong transcription	NHLF	lung
36	chr15:44088400-44092800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr15:44088600-44092200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:44088800-44092000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:44088800-44092000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr15:44088800-44092000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr15:44088800-44092000	Weak transcription	Fetal Brain Male	brain
42	chr15:44088800-44092200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:44088800-44092600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:44089000-44091000	Enhancers	HSMMtube	muscle
45	chr15:44089000-44091200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:44089000-44091200	Weak transcription	Aorta	Aorta
47	chr15:44089000-44092400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:44089200-44091000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr15:44089200-44091000	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:44089200-44091200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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