Variant report

Variant	rs1472989
Chromosome Location	chr15:99864532-99864533
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	EGR1	chr15:99864209-99864863	ECC-1	luminal epithelium:	n/a	chr15:99864712-99864726
2	NR3C1	chr15:99864156-99864597	A549	lung:	n/a	n/a
3	MAX	chr15:99864081-99865273	A549	lung:	n/a	n/a
4	NR3C1	chr15:99864060-99864663	A549	lung:	n/a	n/a
5	TAF1	chr15:99864499-99864788	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr15:99864191-99864670	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr15:99864412-99864796	Hela-S3	cervix:	n/a	n/a
8	RCOR1	chr15:99864229-99864780	Hela-S3	cervix:	n/a	n/a
9	CHD2	chr15:99864230-99864758	Hela-S3	cervix:	n/a	n/a
10	FOXM1	chr15:99863760-99865090	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr15:99863950-99864889	ECC-1	luminal epithelium:	n/a	n/a
12	STAT3	chr15:99864131-99865129	Hela-S3	cervix:	n/a	chr15:99865069-99865080
13	MEF2A	chr15:99864348-99864947	GM12878	blood:	n/a	chr15:99864631-99864640 chr15:99864626-99864647 chr15:99864627-99864642 chr15:99864628-99864643 chr15:99864628-99864642 chr15:99864629-99864640 chr15:99864627-99864642 chr15:99864630-99864641 chr15:99864626-99864647 chr15:99864626-99864647 chr15:99864627-99864643
14	EGR1	chr15:99864267-99865016	HCT-116	colon:	n/a	chr15:99864712-99864726
15	FOXM1	chr15:99863915-99865005	ECC-1	luminal epithelium:	n/a	n/a
16	RUNX3	chr15:99864206-99864867	GM12878	blood:	n/a	n/a
17	CEBPB	chr15:99864160-99865034	Hela-S3	cervix:	n/a	n/a
18	SRF	chr15:99864065-99865055	HCT-116	colon:	n/a	n/a
19	TCF12	chr15:99864009-99864955	ECC-1	luminal epithelium:	n/a	n/a
20	BCL3	chr15:99863946-99865300	A549	lung:	n/a	n/a
21	RAD21	chr15:99864122-99864812	ECC-1	luminal epithelium:	n/a	n/a
22	TCF12	chr15:99864066-99865024	SK-N-SH	brain:	n/a	n/a
23	STAT3	chr15:99864333-99864854	MCF10A-Er-Src	breast:	n/a	n/a
24	POU2F2	chr15:99864494-99864790	GM12891	blood:	n/a	n/a
25	PAX5	chr15:99864222-99864692	GM12891	blood:	n/a	n/a
26	SP1	chr15:99863948-99865275	A549	lung:	n/a	n/a
27	SRF	chr15:99864081-99864828	ECC-1	luminal epithelium:	n/a	n/a
28	RELA	chr15:99864268-99864846	GM19099	blood:	n/a	n/a
29	MTA3	chr15:99864293-99864891	GM12878	blood:	n/a	n/a
30	GTF3C2	chr15:99864021-99864789	Hela-S3	cervix:	n/a	n/a
31	E2F4	chr15:99864233-99865141	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr15:99864231-99864610	SK-N-SH	brain:	n/a	n/a
33	FOS	chr15:99864233-99865031	MCF10A-Er-Src	breast:	n/a	chr15:99864424-99864435 chr15:99864366-99864377 chr15:99864980-99864989
34	NFIC	chr15:99864292-99864903	GM12878	blood:	n/a	n/a
35	CEBPB	chr15:99864148-99864668	A549	lung:	n/a	n/a
36	POLR2A	chr15:99864077-99864831	Hela-S3	cervix:	n/a	n/a
37	TBP	chr15:99864169-99864936	Hela-S3	cervix:	n/a	n/a
38	NFIC	chr15:99864109-99864924	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:99864145-99864829	HCT-116	colon:	n/a	n/a
40	CEBPB	chr15:99864265-99865017	A549	lung:	n/a	n/a
41	FOSL2	chr15:99863627-99865055	A549	lung:	n/a	chr15:99864980-99864989
42	POLR2A	chr15:99864143-99864915	U87	brain:	n/a	n/a
43	MAFK	chr15:99864217-99865210	Hela-S3	cervix:	n/a	chr15:99865125-99865135
44	MAX	chr15:99864242-99864825	Hela-S3	cervix:	n/a	n/a
45	GATA3	chr15:99863925-99865178	A549	lung:	n/a	n/a
46	SMC3	chr15:99864117-99864840	Hela-S3	cervix:	n/a	n/a
47	GABPA	chr15:99863973-99864845	A549	lung:	n/a	n/a
48	MEF2C	chr15:99864315-99864837	GM12878	blood:	n/a	chr15:99864631-99864640 chr15:99864626-99864647 chr15:99864627-99864642 chr15:99864628-99864643 chr15:99864628-99864642 chr15:99864629-99864640 chr15:99864627-99864642 chr15:99864630-99864641 chr15:99864626-99864647 chr15:99864626-99864647 chr15:99864627-99864643
49	POLR2A	chr15:99864259-99864738	MCF10A-Er-Src	breast:	n/a	n/a
50	MAFK	chr15:99864246-99865268	IMR90	lung:	n/a	chr15:99865125-99865135

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99856389..99859314-chr15:99863031..99866195,3	MCF-7	breast:

Variant related genes	Relation type
LRRC28	TF binding region
ENSG00000268730	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1033035	0.99[ASN][1000 genomes]
rs1033036	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10902544	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11247079	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11247081	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853278	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12592075	0.82[AMR][1000 genomes]
rs12913897	0.80[AMR][1000 genomes]
rs1812344	0.83[AMR][1000 genomes]
rs1876927	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175225	0.94[ASN][1000 genomes]
rs28520505	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851679	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3863401	0.98[ASN][1000 genomes]
rs58946939	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6598237	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6598238	0.84[EUR][1000 genomes]
rs7167119	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7167542	0.94[ASN][1000 genomes]
rs7167899	0.86[ASN][1000 genomes]
rs7168227	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7169906	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7171970	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173844	0.92[ASN][1000 genomes]
rs7181739	0.80[AMR][1000 genomes]
rs7182425	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8036160	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8040850	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8041923	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8042249	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8042667	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
14	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
18	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
20	esv3426665	chr15:99862575-99866059	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99793000-99866600	Weak transcription	Gastric	stomach
2	chr15:99833200-99875800	Weak transcription	Thymus	Thymus
3	chr15:99847400-99877200	Weak transcription	Ovary	ovary
4	chr15:99853000-99876000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:99853200-99875400	Weak transcription	Fetal Thymus	thymus
6	chr15:99853600-99875800	Weak transcription	Fetal Intestine Large	intestine
7	chr15:99854400-99876000	Weak transcription	Dnd41	blood
8	chr15:99858600-99876600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:99859400-99906600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:99860400-99864800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:99860600-99865000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:99860600-99867200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr15:99860600-99867200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:99860600-99869200	Enhancers	HepG2	liver
15	chr15:99861000-99865600	Weak transcription	Psoas Muscle	Psoas
16	chr15:99861800-99876600	Weak transcription	Primary T cells from cord blood	blood
17	chr15:99862800-99865400	Flanking Active TSS	A549	lung
18	chr15:99863000-99865400	Enhancers	HSMM	muscle
19	chr15:99863000-99866800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr15:99863200-99881200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:99863200-99899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:99863400-99865200	Enhancers	NHLF	lung
23	chr15:99863600-99866000	Enhancers	Liver	Liver
24	chr15:99863800-99865200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:99863800-99865200	Enhancers	Fetal Heart	heart
26	chr15:99864000-99864600	Enhancers	HUVEC	blood vessel
27	chr15:99864000-99864800	Enhancers	Primary B cells from peripheral blood	blood
28	chr15:99864000-99865200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr15:99864000-99865200	Flanking Active TSS	NHDF-Ad	bronchial
30	chr15:99864200-99864600	Active TSS	Aorta	Aorta
31	chr15:99864200-99864600	Enhancers	Fetal Muscle Leg	muscle
32	chr15:99864200-99864600	Weak transcription	HSMMtube	muscle
33	chr15:99864200-99864800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:99864200-99864800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:99864200-99864800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:99864200-99864800	Active TSS	NH-A	brain
37	chr15:99864200-99865000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:99864200-99865000	Flanking Active TSS	Hela-S3	cervix
39	chr15:99864200-99865800	ZNF genes & repeats	GM12878-XiMat	blood
40	chr15:99864400-99864800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:99864400-99864800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:99864400-99864800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:99864400-99864800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:99864400-99864800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr15:99864400-99864800	Active TSS	Left Ventricle	heart
46	chr15:99864400-99864800	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr15:99864400-99864800	Active TSS	HMEC	breast
48	chr15:99864400-99864800	Flanking Active TSS	NHEK	skin
49	chr15:99864400-99864800	Active TSS	Osteobl	bone
50	chr15:99864400-99902200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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