Variant report

Variant	rs28410121
Chromosome Location	chr15:44070029-44070030
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	CTCF	chr15:44069960-44070110	HCM	heart:	n/a	n/a
2	MYC	chr15:44069657-44070144	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr15:44069148-44070048	MCF10A-Er-Src	breast:	n/a	chr15:44069272-44069281
4	TCF7L2	chr15:44069255-44070046	Hela-S3	cervix:	n/a	n/a
5	E2F6	chr15:44069131-44070149	H1-hESC	embryonic stem cell:	n/a	chr15:44069651-44069662
6	MYC	chr15:44069264-44070038	MCF10A-Er-Src	breast:	n/a	chr15:44069272-44069281
7	E2F6	chr15:44069164-44070173	A549	lung:	n/a	chr15:44069651-44069662
8	RCOR1	chr15:44069257-44070036	Hela-S3	cervix:	n/a	n/a
9	E2F6	chr15:44068953-44070051	K562	blood:	n/a	chr15:44069651-44069662
10	MAX	chr15:44068884-44070213	A549	lung:	n/a	chr15:44069272-44069281
11	CHD2	chr15:44069059-44070042	Hela-S3	cervix:	n/a	chr15:44069237-44069247
12	MAX	chr15:44068476-44070069	H1-hESC	embryonic stem cell:	n/a	chr15:44069272-44069281
13	MYBL2	chr15:44069176-44070065	HepG2	liver:	n/a	n/a
14	TCF12	chr15:44069222-44070061	ECC-1	luminal epithelium:	n/a	n/a
15	KAP1	chr15:44069446-44070044	HEK293	kidney:	n/a	n/a
16	WRNIP1	chr15:44069275-44070051	GM12878	blood:	n/a	n/a
17	RFX5	chr15:44068982-44070064	Hela-S3	cervix:	n/a	n/a
18	TBL1XR1	chr15:44069364-44070144	GM12878	blood:	n/a	n/a
19	CTCF	chr15:44069920-44070070	NHDF-neo	bronchial:	n/a	n/a
20	NFIC	chr15:44069420-44070099	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr15:44067544-44070106	GM12892	blood:	n/a	n/a
22	MAX	chr15:44069008-44070199	A549	lung:	n/a	chr15:44069272-44069281
23	RELA	chr15:44068228-44070039	GM12891	blood:	n/a	n/a
24	POLR2A	chr15:44064991-44070109	GM12878	blood:	n/a	n/a
25	MAX	chr15:44068470-44070125	HepG2	liver:	n/a	chr15:44069272-44069281
26	POLR2A	chr15:44068897-44070084	GM12892	blood:	n/a	n/a
27	CTCF	chr15:44068930-44070159	A549	lung:	n/a	chr15:44069758-44069774 chr15:44069757-44069775
28	STAT5A	chr15:44069211-44070069	GM12878	blood:	n/a	n/a
29	CEBPB	chr15:44069908-44070032	HepG2	liver:	n/a	n/a
30	RUNX3	chr15:44068099-44070145	GM12878	blood:	n/a	chr15:44069713-44069730
31	POLR2A	chr15:44069243-44070036	GM12891	blood:	n/a	n/a
32	HEY1	chr15:44068920-44070109	HepG2	liver:	n/a	n/a
33	POLR2A	chr15:44069109-44070093	IMR90	lung:	n/a	n/a
34	MTA3	chr15:44067495-44070163	GM12878	blood:	n/a	n/a
35	MYC	chr15:44068252-44070111	NB4	blood:	n/a	chr15:44069272-44069281
36	SIN3A	chr15:44067607-44070030	H1-hESC	embryonic stem cell:	n/a	chr15:44069898-44069907
37	POU2F2	chr15:44069361-44070043	GM12891	blood:	n/a	n/a
38	MAX	chr15:44069061-44070128	ECC-1	luminal epithelium:	n/a	chr15:44069272-44069281
39	PAX5	chr15:44069227-44070047	GM12878	blood:	n/a	n/a
40	MTA3	chr15:44069458-44070079	GM12878	blood:	n/a	n/a
41	MAX	chr15:44068806-44070180	HCT-116	colon:	n/a	chr15:44069272-44069281
42	POLR2A	chr15:44068868-44070046	HCT-116	colon:	n/a	n/a
43	POLR2A	chr15:44069207-44070125	Hela-S3	cervix:	n/a	n/a
44	EGR1	chr15:44068892-44070032	HCT-116	colon:	n/a	chr15:44069273-44069282 chr15:44069270-44069283 chr15:44069272-44069282 chr15:44069220-44069234 chr15:44069223-44069236 chr15:44069270-44069283 chr15:44069272-44069282 chr15:44069270-44069283 chr15:44069270-44069284 chr15:44069271-44069282 chr15:44069270-44069283
45	TBP	chr15:44068893-44070061	GM12878	blood:	n/a	n/a
46	MYC	chr15:44069028-44070075	Hela-S3	cervix:	n/a	chr15:44069272-44069281
47	POLR2A	chr15:44068960-44070077	MCF10A-Er-Src	breast:	n/a	n/a
48	EBF1	chr15:44068141-44070065	GM12878	blood:	n/a	chr15:44068925-44068935 chr15:44068495-44068506 chr15:44068534-44068545 chr15:44068924-44068937 chr15:44068926-44068935
49	MAX	chr15:44069055-44070180	ECC-1	luminal epithelium:	n/a	chr15:44069272-44069281
50	POLR2A	chr15:44068954-44070111	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44066200..44071612-chr15:44082403..44086035,7	K562	blood:
2	chr15:44060010..44065607-chr15:44066577..44070669,7	K562	blood:
3	chr15:44067716..44069540-chr15:44069766..44073252,3	MCF-7	breast:
4	chr15:44067949..44070096-chr15:44073710..44075913,2	MCF-7	breast:
5	chr15:44069584..44070253-chr5:33440643..33441634,2	Hela-S3	cervix:
6	chr15:44065408..44074556-chr15:44080543..44088380,28	MCF-7	breast:
7	chr15:44062113..44074982-chr15:44088756..44097846,29	MCF-7	breast:
8	chr15:44065227..44073214-chr15:44081584..44094479,46	MCF-7	breast:
9	chr15:44069380..44070317-chr5:16465731..16466497,2	Hela-S3	cervix:
10	chr15:44060550..44065898-chr15:44066868..44071265,7	MCF-7	breast:
11	chr15:44068154..44070774-chr15:44115060..44118766,3	K562	blood:
12	chr15:44037743..44040701-chr15:44068299..44070156,3	MCF-7	breast:

Variant related genes	Relation type
ELL3	TF binding region
ENSG00000205771	Chromatin interaction
ENSG00000140259	Chromatin interaction
ENSG00000242028	Chromatin interaction
ENSG00000221792	Chromatin interaction
ENSG00000113407	Chromatin interaction
ENSG00000173545	Chromatin interaction
ENSG00000167004	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000268488	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000249572	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10163069	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11070411	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12443084	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17727853	1.00[CEU][hapmap]
rs17795279	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2412821	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2918947	0.81[EUR][1000 genomes]
rs2930529	0.93[EUR][1000 genomes]
rs2930530	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs3102448	0.86[EUR][1000 genomes]
rs3110081	0.86[EUR][1000 genomes]
rs35822148	0.85[EUR][1000 genomes]
rs3862143	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3986209	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs514311	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs528764	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs541871	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs62018940	0.89[EUR][1000 genomes]
rs62018944	0.87[EUR][1000 genomes]
rs6493090	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.88[EUR][1000 genomes]
rs678084	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs7174241	0.84[GIH][hapmap];0.88[MKK][hapmap]
rs7174260	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7178230	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8030536	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs8038068	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28410121	ZSCAN29	cis	multi-tissue	Pritchard
rs28410121	TUBGCP4	cis	parietal	SCAN
rs28410121	WDR76	cis	parietal	SCAN
rs28410121	TGM5	cis	lymphoblastoid	seeQTL
rs28410121	MAPKBP1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44068000-44070200	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr15:44068000-44070200	Active TSS	Rectal Smooth Muscle	rectum
3	chr15:44068200-44070200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr15:44068200-44070200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr15:44068200-44070200	Active TSS	K562	blood
6	chr15:44068400-44070200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:44068400-44070200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:44068400-44070200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr15:44068400-44070200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:44068400-44070200	Active TSS	Fetal Intestine Small	intestine
11	chr15:44068400-44070200	Flanking Active TSS	Fetal Muscle Trunk	muscle
12	chr15:44068400-44070200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr15:44068400-44070200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr15:44068400-44070200	Active TSS	HepG2	liver
15	chr15:44068400-44070200	Active TSS	NHDF-Ad	bronchial
16	chr15:44068400-44070400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:44068600-44070200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:44068600-44070200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:44068600-44070200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr15:44068600-44070200	Active TSS	Brain Hippocampus Middle	brain
21	chr15:44068600-44070200	Enhancers	Fetal Brain Male	brain
22	chr15:44068600-44070200	Active TSS	A549	lung
23	chr15:44068600-44070200	Active TSS	HSMM	muscle
24	chr15:44068800-44070200	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr15:44068800-44070200	Active TSS	H1 Cell Line	embryonic stem cell
26	chr15:44068800-44070200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:44068800-44070200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr15:44068800-44070200	Active TSS	Brain Anterior Caudate	brain
29	chr15:44068800-44070200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:44068800-44070200	Active TSS	Fetal Lung	lung
31	chr15:44068800-44070200	Active TSS	Lung	lung
32	chr15:44068800-44073200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:44069000-44070200	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr15:44069000-44070200	Active TSS	Placenta Amnion	Placenta Amnion
35	chr15:44069000-44070200	Active TSS	Right Atrium	heart
36	chr15:44069000-44070200	Active TSS	NHLF	lung
37	chr15:44069400-44070200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr15:44069400-44070200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr15:44069400-44070200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr15:44069400-44070200	Flanking Active TSS	NH-A	brain
41	chr15:44069600-44070200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:44069600-44070200	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr15:44069600-44070200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr15:44069600-44070200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr15:44069600-44070200	Flanking Active TSS	Placenta	Placenta
46	chr15:44069600-44070200	Flanking Active TSS	HMEC	breast
47	chr15:44069600-44070200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr15:44069800-44070200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:44069800-44070200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:44069800-44070200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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