Variant report

Variant	rs1073378
Chromosome Location	chr20:13228071-13228072
allele	A/G
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	BCL11A	chr20:13228024-13228227	GM12878	blood:	n/a	n/a
2	BCLAF1	chr20:13227848-13228366	GM12878	blood:	n/a	n/a
3	IKZF1	chr20:13227968-13228662	GM12878	blood:	n/a	n/a
4	ELF1	chr20:13227997-13228238	GM12878	blood:	n/a	n/a
5	IRF4	chr20:13227965-13228363	GM12878	blood:	n/a	n/a
6	YY1	chr20:13227944-13228231	GM12878	blood:	n/a	n/a
7	FOSL2	chr20:13227939-13228283	MCF-7	breast:	n/a	n/a
8	SP1	chr20:13227898-13228316	GM12878	blood:	n/a	n/a
9	EP300	chr20:13228025-13228636	GM12878	blood:	n/a	n/a
10	BATF	chr20:13227971-13228436	GM12878	blood:	n/a	chr20:13228049-13228062 chr20:13228309-13228318
11	TCF3	chr20:13228035-13228180	GM12878	blood:	n/a	n/a
12	POLR2A	chr20:13227881-13228398	HUVEC	blood vessel:	n/a	n/a
13	HDAC2	chr20:13227895-13228286	MCF-7	breast:	n/a	n/a
14	EP300	chr20:13227982-13228494	GM12878	blood:	n/a	n/a
15	PAX5	chr20:13227906-13228394	GM12878	blood:	n/a	n/a
16	NFIC	chr20:13227884-13228554	GM12878	blood:	n/a	n/a
17	JUND	chr20:13227911-13228697	HCT-116	colon:	n/a	n/a
18	NR2F2	chr20:13227932-13228261	MCF-7	breast:	n/a	n/a
19	NFATC1	chr20:13227932-13228429	GM12878	blood:	n/a	n/a
20	POU2F2	chr20:13227843-13228399	GM12891	blood:	n/a	n/a
21	BCLAF1	chr20:13227948-13228349	GM12878	blood:	n/a	n/a
22	RUNX3	chr20:13227842-13228845	GM12878	blood:	n/a	chr20:13228657-13228666 chr20:13228657-13228666
23	MYC	chr20:13228064-13228229	HUVEC	blood vessel:	n/a	n/a
24	ATF2	chr20:13227864-13228573	GM12878	blood:	n/a	n/a
25	PML	chr20:13227925-13228429	GM12878	blood:	n/a	n/a
26	BCL11A	chr20:13227920-13228337	GM12878	blood:	n/a	n/a
27	ESR1	chr20:13227868-13228216	T-47D	breast:	n/a	chr20:13228002-13228019
28	EGR1	chr20:13228053-13228185	GM12878	blood:	n/a	n/a
29	EBF1	chr20:13228042-13228611	GM12878	blood:	n/a	n/a
30	PAX5	chr20:13227990-13228244	GM12878	blood:	n/a	n/a
31	CHD2	chr20:13227947-13228291	GM12878	blood:	n/a	n/a
32	EP300	chr20:13227873-13228252	MCF-7	breast:	n/a	n/a
33	GATA1	chr20:13227854-13228714	PBDE	blood:	n/a	chr20:13228394-13228404 chr20:13228056-13228073
34	SIN3AK20	chr20:13227849-13228427	MCF-7	breast:	n/a	n/a
35	SP1	chr20:13227900-13228766	HCT-116	colon:	n/a	n/a
36	RUNX3	chr20:13227861-13228832	GM12878	blood:	n/a	chr20:13228657-13228666 chr20:13228657-13228666
37	NR2F2	chr20:13227913-13228221	K562	blood:	n/a	n/a
38	NFIC	chr20:13227861-13228518	GM12878	blood:	n/a	n/a
39	POU2F2	chr20:13227899-13228336	GM12891	blood:	n/a	n/a
40	FOS	chr20:13227884-13228755	HUVEC	blood vessel:	n/a	n/a
41	ETS1	chr20:13227879-13228566	GM12878	blood:	n/a	chr20:13228394-13228408 chr20:13228395-13228406 chr20:13228393-13228406 chr20:13228394-13228403
42	GATA2	chr20:13227869-13228809	HUVEC	blood vessel:	n/a	chr20:13228394-13228404 chr20:13228056-13228073
43	POLR2A	chr20:13227925-13228290	HUVEC	blood vessel:	n/a	n/a
44	EP300	chr20:13227987-13228245	GM12878	blood:	n/a	n/a
45	IRF4	chr20:13227911-13228378	GM12878	blood:	n/a	n/a
46	TCF3	chr20:13227926-13228446	GM12878	blood:	n/a	chr20:13228330-13228346
47	ZEB1	chr20:13227979-13228256	GM12878	blood:	n/a	n/a
48	POLR2A	chr20:13227962-13228223	HUVEC	blood vessel:	n/a	n/a
49	RELA	chr20:13227952-13228636	GM19099	blood:	n/a	n/a
50	MTA3	chr20:13227841-13228518	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13222224..13226467-chr20:13226832..13229125,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225956	TF binding region
ENSG00000225956	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1060580	0.90[ASN][1000 genomes]
rs1073377	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12624775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12625420	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12625749	0.95[EUR][1000 genomes]
rs1407333	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1407334	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1407336	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1407337	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1407338	0.91[ASN][1000 genomes]
rs1819168	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1819169	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1819170	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1923347	0.82[CEU][hapmap];0.93[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1923348	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34656017	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35637805	0.89[ASN][1000 genomes]
rs4814206	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4814207	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4814208	0.81[CEU][hapmap];0.93[CHB][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4814209	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814210	0.93[CHB][hapmap];0.91[ASN][1000 genomes]
rs57877502	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6105055	0.86[CHB][hapmap];0.90[ASN][1000 genomes]
rs6105057	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6105058	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6109764	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6109767	0.90[ASN][1000 genomes]
rs6109768	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109769	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109770	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109772	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109773	0.86[CHB][hapmap];0.90[ASN][1000 genomes]
rs6109774	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6109775	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6109776	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6109777	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109778	0.97[ASN][1000 genomes]
rs6109779	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109780	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6109781	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6109782	0.96[ASN][1000 genomes]
rs6131455	0.91[ASN][1000 genomes]
rs6131456	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6134825	0.90[ASN][1000 genomes]
rs6134826	0.90[ASN][1000 genomes]
rs6134827	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6134830	0.80[EUR][1000 genomes]
rs6134831	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134834	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134835	0.97[ASN][1000 genomes]
rs6134836	0.89[ASN][1000 genomes]
rs721243	0.81[CEU][hapmap];0.93[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7263654	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv912685	chr20:13134768-13234124	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv912686	chr20:13205338-13311983	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1060853	chr20:13215866-13284603	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1058035	chr20:13217890-13249342	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	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	chr20:13203600-13229800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr20:13218800-13243200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr20:13223000-13229600	Enhancers	Liver	Liver
4	chr20:13224800-13229800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr20:13225000-13231000	Weak transcription	Pancreas	Pancrea
6	chr20:13225200-13228200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr20:13225200-13229800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr20:13226000-13229400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:13226200-13229800	Enhancers	HepG2	liver
10	chr20:13226200-13233800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr20:13226200-13233800	Weak transcription	Placenta	Placenta
12	chr20:13226400-13228200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr20:13226600-13228400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr20:13226800-13229800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr20:13227000-13228200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr20:13227000-13228400	Enhancers	Primary hematopoietic stem cells	blood
17	chr20:13227000-13228400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr20:13227000-13229000	Enhancers	HUVEC	blood vessel
19	chr20:13227000-13230400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr20:13227000-13231600	Enhancers	Fetal Thymus	thymus
21	chr20:13227200-13228200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr20:13227200-13228200	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr20:13227200-13228400	Enhancers	Thymus	Thymus
24	chr20:13227200-13229800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr20:13227400-13231200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:13227600-13229000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr20:13227600-13229600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr20:13227800-13228200	Enhancers	GM12878-XiMat	blood
29	chr20:13227800-13228800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr20:13227800-13229000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr20:13227800-13229400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr20:13227800-13229600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr20:13228000-13228200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr20:13228000-13228400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr20:13228000-13228400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr20:13228000-13228400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr20:13228000-13228600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr20:13228000-13228600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr20:13228000-13228600	Enhancers	Osteobl	bone
40	chr20:13228000-13228800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr20:13228000-13228800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr20:13228000-13228800	Enhancers	Primary B cells from peripheral blood	blood
43	chr20:13228000-13228800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr20:13228000-13228800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr20:13228000-13228800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr20:13228000-13228800	Enhancers	Lung	lung
47	chr20:13228000-13229000	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr20:13228000-13229000	Flanking Active TSS	NHEK	skin
49	chr20:13228000-13229200	Flanking Active TSS	HMEC	breast
50	chr20:13228000-13229600	Flanking Active TSS	Dnd41	blood

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