Variant report

Variant	rs28373413
Chromosome Location	chr5:177540360-177540361
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	CTCF	chr5:177540197-177540395	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:177540328-177540897	H1-neurons	neurons:	n/a	n/a
3	CTCF	chr5:177540254-177540493	T-47D	breast:	n/a	n/a
4	POU2F2	chr5:177540359-177540884	GM12878	blood:	n/a	chr5:177540824-177540836
5	NR2F2	chr5:177540271-177540714	K562	blood:	n/a	n/a
6	USF2	chr5:177540123-177541389	GM12878	blood:	n/a	chr5:177540630-177540646
7	MXI1	chr5:177540178-177540750	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr5:177540117-177540897	K562	blood:	n/a	chr5:177540465-177540474 chr5:177540790-177540801 chr5:177540816-177540827 chr5:177540480-177540494 chr5:177540628-177540642 chr5:177540460-177540474 chr5:177540289-177540303
9	POLR2A	chr5:177540136-177541529	K562	blood:	n/a	n/a
10	CTCF	chr5:177540206-177540465	MCF-7	breast:	n/a	n/a
11	POLR2A	chr5:177540170-177540785	GM12878	blood:	n/a	n/a
12	MAX	chr5:177540150-177540852	K562	blood:	n/a	chr5:177540283-177540292
13	CTCF	chr5:177540221-177540420	MCF-7	breast:	n/a	n/a
14	RCOR1	chr5:177539580-177541670	K562	blood:	n/a	n/a
15	NFYB	chr5:177540318-177540750	GM12878	blood:	n/a	n/a
16	CTCF	chr5:177540218-177540402	A549	lung:	n/a	n/a
17	SMC3	chr5:177540249-177540693	GM12878	blood:	n/a	n/a
18	RAD21	chr5:177540130-177540806	MCF-7	breast:	n/a	n/a
19	PAX5	chr5:177540086-177540770	GM12892	blood:	n/a	chr5:177540110-177540119 chr5:177540259-177540268
20	ZEB1	chr5:177540310-177540632	GM12878	blood:	n/a	n/a
21	RELA	chr5:177540013-177542731	GM15510	blood:	n/a	chr5:177540530-177540539 chr5:177540530-177540539
22	ETS1	chr5:177540238-177540791	K562	blood:	n/a	chr5:177540480-177540491
23	PML	chr5:177539853-177540840	GM12878	blood:	n/a	n/a
24	RCOR1	chr5:177539802-177540741	GM12878	blood:	n/a	n/a
25	BHLHE40	chr5:177540090-177540868	K562	blood:	n/a	chr5:177540630-177540646
26	POLR2A	chr5:177540223-177540828	MCF-7	breast:	n/a	n/a
27	MAX	chr5:177540066-177540822	K562	blood:	n/a	chr5:177540283-177540292
28	POLR2A	chr5:177540147-177543786	H1-hESC	embryonic stem cell:	n/a	n/a
29	PAX5	chr5:177540120-177540769	GM12878	blood:	n/a	chr5:177540259-177540268
30	MAX	chr5:177539977-177540868	ECC-1	luminal epithelium:	n/a	chr5:177540283-177540292
31	MAX	chr5:177540055-177541040	H1-hESC	embryonic stem cell:	n/a	chr5:177540283-177540292
32	CTCF	chr5:177540284-177540418	GM20000	blood:	n/a	n/a
33	YY1	chr5:177540166-177540678	ECC-1	luminal epithelium:	n/a	chr5:177540465-177540474 chr5:177540480-177540494 chr5:177540628-177540642 chr5:177540460-177540474 chr5:177540289-177540303
34	YY1	chr5:177540153-177540784	H1-hESC	embryonic stem cell:	n/a	chr5:177540465-177540474 chr5:177540480-177540494 chr5:177540628-177540642 chr5:177540460-177540474 chr5:177540289-177540303
35	REST	chr5:177539973-177540844	H1-neurons	neurons:	n/a	chr5:177540711-177540721
36	CCNT2	chr5:177540123-177541693	K562	blood:	n/a	chr5:177541562-177541571 chr5:177540483-177540492 chr5:177541203-177541212 chr5:177540790-177540799 chr5:177541358-177541367 chr5:177540826-177540835 chr5:177541035-177541044 chr5:177540816-177540825 chr5:177540465-177540474
37	POLR2A	chr5:177540142-177541426	GM12892	blood:	n/a	n/a
38	SP1	chr5:177540236-177540895	H1-hESC	embryonic stem cell:	n/a	chr5:177540822-177540836 chr5:177540464-177540474 chr5:177540464-177540473 chr5:177540825-177540837 chr5:177540827-177540836 chr5:177540464-177540478 chr5:177540280-177540290 chr5:177540825-177540837 chr5:177540832-177540841 chr5:177540464-177540474 chr5:177540538-177540549 chr5:177540463-177540475 chr5:177540578-177540589 chr5:177540465-177540474 chr5:177540463-177540475 chr5:177540826-177540836 chr5:177540464-177540473 chr5:177540816-177540825
39	CTCF	chr5:177540212-177540423	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr5:177540301-177540411	MCF-7	breast:	n/a	n/a
41	ELF1	chr5:177540191-177540753	GM12878	blood:	n/a	chr5:177540374-177540386 chr5:177540737-177540749 chr5:177540480-177540492
42	MAX	chr5:177540028-177541206	ECC-1	luminal epithelium:	n/a	chr5:177540283-177540292
43	NANOG	chr5:177540216-177540835	H1-hESC	embryonic stem cell:	n/a	n/a
44	TAF1	chr5:177540347-177540788	GM12878	blood:	n/a	n/a
45	CTCF	chr5:177540240-177540390	GM12873	blood:	n/a	n/a
46	E2F6	chr5:177540066-177540964	K562	blood:	n/a	chr5:177540465-177540474 chr5:177540629-177540639 chr5:177540639-177540648
47	RUNX3	chr5:177539922-177540765	GM12878	blood:	n/a	n/a
48	CTCF	chr5:177540317-177540413	GM13977	blood:	n/a	n/a
49	POLR2A	chr5:177540084-177541223	ECC-1	luminal epithelium:	n/a	n/a
50	JUND	chr5:177539582-177541064	K562	blood:	n/a	chr5:177540360-177540374 chr5:177540517-177540529 chr5:177540523-177540537 chr5:177540466-177540475 chr5:177540519-177540527 chr5:177540902-177540913 chr5:177540517-177540528 chr5:177539680-177539691 chr5:177540515-177540526

No.	Distal block	Cell Line	Cell type
1	chr5:177025398..177027289-chr5:177540105..177542434,2	MCF-7	breast:
2	chr5:177539043..177545979-chr5:177577141..177584026,12	K562	blood:
3	chr5:177540128..177541993-chrX:153630479..153632171,2	MCF-7	breast:
4	chr5:177538337..177541901-chr5:177630904..177633261,3	K562	blood:
5	chr11:62607697..62609963-chr5:177539195..177541814,2	MCF-7	breast:
6	chr5:177539791..177542194-chr5:177578689..177582162,4	K562	blood:
7	chr5:177018435..177020960-chr5:177539226..177540753,2	MCF-7	breast:

Variant related genes	Relation type
N4BP3	TF binding region
ENSG00000184840	Chromatin interaction
ENSG00000145912	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000027847	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10066437	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv883186	chr5:177376317-177549491	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
4	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv600391	chr5:177488281-177549491	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
7	nsv462567	chr5:177505021-177572927	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv471058	chr5:177505021-177572927	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
9	nsv600392	chr5:177505021-177572927	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
11	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv883191	chr5:177535370-177551985	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
13	nsv883192	chr5:177535370-177564346	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	esv3443720	chr5:177539696-177541944	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177539600-177541400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
2	chr5:177539800-177540400	Flanking Active TSS	Primary B cells from peripheral blood	blood
3	chr5:177539800-177540400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:177539800-177540400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr5:177539800-177540400	Flanking Active TSS	GM12878-XiMat	blood
6	chr5:177539800-177541000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:177539800-177541000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:177539800-177541000	Bivalent/Poised TSS	Fetal Brain Female	brain
9	chr5:177539800-177541200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:177539800-177541400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr5:177539800-177541600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:177539800-177541600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr5:177539800-177541800	Active TSS	H1 Cell Line	embryonic stem cell
14	chr5:177539800-177541800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr5:177539800-177541800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr5:177539800-177541800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr5:177539800-177542000	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr5:177539800-177542800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr5:177539800-177543400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr5:177540000-177540400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr5:177540000-177540400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr5:177540000-177540400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr5:177540000-177540400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:177540000-177540400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:177540000-177540400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:177540000-177540400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
27	chr5:177540000-177540400	Flanking Active TSS	Placenta	Placenta
28	chr5:177540000-177540400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
29	chr5:177540000-177540400	Bivalent Enhancer	Stomach Mucosa	stomach
30	chr5:177540000-177540400	Bivalent Enhancer	Spleen	Spleen
31	chr5:177540000-177540600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:177540000-177540600	Enhancers	Rectal Smooth Muscle	rectum
33	chr5:177540000-177540800	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:177540000-177540800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:177540000-177540800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr5:177540000-177541000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:177540000-177541000	Active TSS	Placenta Amnion	Placenta Amnion
38	chr5:177540000-177541000	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr5:177540000-177541000	Active TSS	Right Ventricle	heart
40	chr5:177540000-177541000	Bivalent/Poised TSS	NH-A	brain
41	chr5:177540000-177541200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:177540000-177541200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr5:177540000-177541200	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr5:177540000-177541200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
45	chr5:177540000-177541200	Bivalent/Poised TSS	A549	lung
46	chr5:177540000-177541200	Active TSS	HUVEC	blood vessel
47	chr5:177540000-177541400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
48	chr5:177540000-177541800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:177540000-177541800	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr5:177540000-177541800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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