Variant report

Variant	rs72934806
Chromosome Location	chr3:50397307-50397308
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	MYC	chr3:50396672-50397327	NB4	blood:	n/a	n/a
2	ELF1	chr3:50396792-50397400	A549	lung:	n/a	chr3:50396972-50396981
3	BHLHE40	chr3:50396778-50397463	K562	blood:	n/a	chr3:50396966-50396982
4	USF2	chr3:50396730-50397327	Hela-S3	cervix:	n/a	chr3:50396966-50396982
5	POLR2A	chr3:50394527-50397849	MCF10A-Er-Src	breast:	n/a	n/a
6	ELF1	chr3:50396252-50397407	GM12878	blood:	n/a	chr3:50396972-50396981
7	GABPA	chr3:50396458-50397642	MCF-7	breast:	n/a	chr3:50396957-50396966 chr3:50396955-50396966 chr3:50396952-50396966
8	YY1	chr3:50396895-50397344	GM12892	blood:	n/a	chr3:50396973-50396984
9	MTA3	chr3:50396237-50397582	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:50395646-50397333	Hela-S3	cervix:	n/a	n/a
11	STAT5A	chr3:50396573-50397508	GM12878	blood:	n/a	chr3:50397189-50397201
12	SIX5	chr3:50396856-50397342	K562	blood:	n/a	chr3:50397080-50397089 chr3:50397082-50397091 chr3:50397143-50397152 chr3:50397145-50397154
13	STAT1	chr3:50396792-50397528	GM12878	blood:	n/a	chr3:50397189-50397201
14	KAP1	chr3:50396741-50397499	U2OS	brain:	n/a	n/a
15	POLR2A	chr3:50395832-50397382	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr3:50396624-50397349	GM12878	blood:	n/a	n/a
17	ELF1	chr3:50396555-50397480	SK-N-SH	brain:	n/a	chr3:50396972-50396981
18	GABPA	chr3:50396600-50397456	HL-60	blood:	n/a	chr3:50396957-50396966 chr3:50396955-50396966 chr3:50396952-50396966
19	TCF12	chr3:50396894-50397333	A549	lung:	n/a	n/a
20	MBD4	chr3:50396619-50397372	HepG2	liver:	n/a	n/a
21	RELA	chr3:50396818-50397328	GM19099	blood:	n/a	n/a
22	MAX	chr3:50396297-50397367	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr3:50396189-50397385	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr3:50396601-50397385	ECC-1	luminal epithelium:	n/a	n/a
25	RCOR1	chr3:50397008-50397359	K562	blood:	n/a	n/a
26	POLR2A	chr3:50395691-50397692	MCF10A-Er-Src	breast:	n/a	n/a
27	MAX	chr3:50396255-50397328	ECC-1	luminal epithelium:	n/a	n/a
28	ELF1	chr3:50396694-50397340	HepG2	liver:	n/a	chr3:50396972-50396981
29	REST	chr3:50396282-50397464	H1-neurons	neurons:	n/a	chr3:50396877-50396890 chr3:50396950-50396963
30	RCOR1	chr3:50396726-50397356	Hela-S3	cervix:	n/a	n/a
31	YY1	chr3:50396807-50397330	K562	blood:	n/a	chr3:50396973-50396984
32	ELF1	chr3:50396405-50397507	HCT-116	colon:	n/a	chr3:50396972-50396981
33	BCLAF1	chr3:50396786-50397373	GM12878	blood:	n/a	chr3:50396969-50396982
34	POLR2A	chr3:50396235-50397307	HCT-116	colon:	n/a	n/a
35	JUN	chr3:50396588-50397379	K562	blood:	n/a	n/a
36	NFIC	chr3:50396814-50397311	HepG2	liver:	n/a	n/a
37	YY1	chr3:50396123-50397368	HepG2	liver:	n/a	chr3:50396973-50396984
38	CTCF	chr3:50397300-50397360	GM19239	blood:	n/a	n/a
39	POLR2A	chr3:50396567-50397328	PFSK-1	brain:	n/a	n/a
40	KAP1	chr3:50396583-50397481	HEK293	kidney:	n/a	n/a
41	CHD2	chr3:50396945-50397406	K562	blood:	n/a	n/a
42	POLR2A	chr3:50396674-50397355	GM12891	blood:	n/a	n/a
43	CREB1	chr3:50396711-50397419	GM12878	blood:	n/a	n/a
44	RFX5	chr3:50396677-50397357	Hela-S3	cervix:	n/a	n/a
45	RELA	chr3:50396746-50397357	GM18951	blood:	n/a	n/a
46	MAX	chr3:50396650-50397375	GM12878	blood:	n/a	n/a
47	CREB1	chr3:50396595-50397392	HepG2	liver:	n/a	n/a
48	MYBL2	chr3:50396824-50397324	HepG2	liver:	n/a	n/a
49	ELF1	chr3:50396404-50397334	GM12878	blood:	n/a	chr3:50396972-50396981
50	TBP	chr3:50396741-50397307	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50394476..50397336-chr3:50402508..50404980,5	MCF-7	breast:
2	chr3:50358941..50361701-chr3:50396606..50398793,2	MCF-7	breast:
3	chr3:50373336..50376121-chr3:50395555..50398512,4	K562	blood:
4	chr3:50397057..50398751-chr3:50648242..50650583,2	MCF-7	breast:
5	chr3:50386112..50390194-chr3:50392847..50399521,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYB561D2-2	chr3:50396941-50400230	NONHSAT089837

Variant related genes	Relation type
TMEM115	TF binding region
ENSG00000068001	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000114388	Chromatin interaction
ENSG00000114395	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000272104	Chromatin interaction
ENSG00000271858	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000007402	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12485286	0.86[AFR][1000 genomes]
rs2233482	1.00[AMR][1000 genomes]
rs58780990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59556423	1.00[AMR][1000 genomes]
rs60983897	1.00[AMR][1000 genomes]
rs61275090	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61689858	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61737738	1.00[AMR][1000 genomes]
rs72932956	1.00[AMR][1000 genomes]
rs72932962	1.00[AMR][1000 genomes]
rs72932964	1.00[AMR][1000 genomes]
rs72932983	1.00[AMR][1000 genomes]
rs72932994	0.83[AFR][1000 genomes]
rs72934803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934809	0.93[AFR][1000 genomes]
rs72934811	0.86[AFR][1000 genomes]
rs72934814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934824	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934827	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934830	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs928946	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
12	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
13	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
15	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
16	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
18	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50393400-50397600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:50394800-50397400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:50395600-50397400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr3:50395600-50397400	Active TSS	HSMMtube	muscle
5	chr3:50395600-50397400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr3:50395600-50397600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:50395800-50397400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr3:50395800-50397400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr3:50395800-50397400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr3:50395800-50397400	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr3:50395800-50397600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:50395800-50397600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr3:50395800-50397600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:50395800-50397600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:50395800-50397600	Active TSS	HSMM	muscle
16	chr3:50396000-50397600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:50396000-50397600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:50396000-50397600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:50396000-50397800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:50396200-50397400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:50396200-50397400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr3:50396200-50397400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:50396200-50397400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:50396200-50397400	Active TSS	Left Ventricle	heart
25	chr3:50396200-50397400	Active TSS	HMEC	breast
26	chr3:50396200-50397600	Active TSS	Psoas Muscle	Psoas
27	chr3:50396200-50397600	Active TSS	Rectal Smooth Muscle	rectum
28	chr3:50396400-50397400	Active TSS	Brain Substantia Nigra	brain
29	chr3:50396400-50397400	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr3:50396400-50397600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:50396400-50397600	Active TSS	Fetal Brain Female	brain
32	chr3:50396400-50397800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:50396600-50397400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:50396600-50397600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:50396800-50397400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:50396800-50397400	Active TSS	Colonic Mucosa	Colon
37	chr3:50397000-50397400	Enhancers	Primary hematopoietic stem cells	blood
38	chr3:50397000-50397400	Flanking Active TSS	Fetal Thymus	thymus
39	chr3:50397000-50397400	Enhancers	Ovary	ovary
40	chr3:50397000-50397400	Active TSS	Right Atrium	heart
41	chr3:50397000-50397400	Enhancers	Stomach Mucosa	stomach
42	chr3:50397000-50397600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:50397000-50397600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:50397000-50397600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:50397000-50397600	Active TSS	Brain Germinal Matrix	brain
46	chr3:50397000-50397600	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr3:50397000-50397800	Enhancers	Pancreas	Pancrea
48	chr3:50397000-50401600	Weak transcription	Lung	lung
49	chr3:50397000-50402000	Weak transcription	Fetal Heart	heart
50	chr3:50397200-50397400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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