Variant report

Variant	rs16868773
Chromosome Location	chr5:89826363-89826364
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	ZNF143	chr5:89824771-89826429	K562	blood:	n/a	n/a
2	IRF1	chr5:89825195-89826614	K562	blood:	n/a	chr5:89826531-89826543 chr5:89826042-89826051
3	E2F4	chr5:89825944-89826454	MCF10A-Er-Src	breast:	n/a	n/a
4	CTCF	chr5:89824880-89826659	SK-N-SH	brain:	n/a	chr5:89825024-89825032
5	CTCF	chr5:89825304-89826369	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:89821851-89826472	K562	blood:	n/a	n/a
7	RFX5	chr5:89824759-89826402	Hela-S3	cervix:	n/a	n/a
8	EP300	chr5:89824639-89826652	K562	blood:	n/a	chr5:89826147-89826156 chr5:89825539-89825555
9	TRIM28	chr5:89825033-89826579	K562	blood:	n/a	chr5:89826149-89826158
10	CTCF	chr5:89826300-89826450	HepG2	liver:	n/a	n/a
11	CTCF	chr5:89826220-89826370	Caco-2	colon:	n/a	n/a
12	CUX1	chr5:89825849-89826509	K562	blood:	n/a	n/a
13	CTCF	chr5:89826220-89826370	SK-N-SH_RA	brain:	n/a	n/a
14	FOS	chr5:89825247-89826371	HUVEC	blood vessel:	n/a	chr5:89826147-89826157 chr5:89826147-89826157 chr5:89826149-89826156 chr5:89826148-89826156 chr5:89826148-89826156 chr5:89826147-89826157
15	RAD21	chr5:89825075-89826375	HCT-116	colon:	n/a	chr5:89825493-89825505
16	CTCF	chr5:89826305-89826416	GM10266	blood:	n/a	n/a
17	MAFF	chr5:89825803-89826506	K562	blood:	n/a	n/a
18	ZNF384	chr5:89825326-89826377	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:89824519-89826437	K562	blood:	n/a	n/a
20	MAFK	chr5:89825630-89826413	K562	blood:	n/a	n/a
21	KAP1	chr5:89825707-89826455	U2OS	brain:	n/a	chr5:89826149-89826158
22	MAZ	chr5:89824114-89826488	IMR90	lung:	n/a	chr5:89826147-89826156
23	ZMIZ1	chr5:89824494-89826595	K562	blood:	n/a	n/a
24	RAD21	chr5:89825701-89826364	A549	lung:	n/a	n/a
25	JUN	chr5:89823293-89826982	K562	blood:	n/a	chr5:89826147-89826157 chr5:89826147-89826157 chr5:89826149-89826156 chr5:89826148-89826156 chr5:89826148-89826156 chr5:89826147-89826157
26	RAD21	chr5:89825694-89826401	MCF-7	breast:	n/a	n/a
27	CTCF	chr5:89825549-89826478	K562	blood:	n/a	n/a
28	JUND	chr5:89825864-89826389	HepG2	liver:	n/a	chr5:89826147-89826157 chr5:89826147-89826157 chr5:89826146-89826157 chr5:89826149-89826156 chr5:89826148-89826156 chr5:89826148-89826156 chr5:89826147-89826157
29	SMC3	chr5:89825620-89826450	K562	blood:	n/a	n/a
30	ARID3A	chr5:89825821-89826660	K562	blood:	n/a	n/a
31	RAD21	chr5:89824488-89826719	SK-N-SH	brain:	n/a	chr5:89825073-89825082 chr5:89825493-89825505
32	CREB1	chr5:89824456-89826363	K562	blood:	n/a	n/a
33	SMC3	chr5:89824820-89826683	SK-N-SH	brain:	n/a	n/a
34	JUND	chr5:89824574-89826427	K562	blood:	n/a	chr5:89826147-89826157 chr5:89826147-89826157 chr5:89826146-89826157 chr5:89826149-89826156 chr5:89826148-89826156 chr5:89826148-89826156 chr5:89826147-89826157
35	CTCF	chr5:89825610-89826400	HCT-116	colon:	n/a	n/a
36	RAD21	chr5:89824902-89826374	HCT-116	colon:	n/a	chr5:89825073-89825082 chr5:89825493-89825505
37	TEAD4	chr5:89824421-89826475	K562	blood:	n/a	n/a
38	RCOR1	chr5:89824388-89826408	K562	blood:	n/a	n/a
39	FOXM1	chr5:89825723-89826455	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr5:89824311-89826445	PBDE	blood:	n/a	n/a
41	HCFC1	chr5:89824457-89826625	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr5:89825607-89826465	IMR90	lung:	n/a	n/a
43	CTCF	chr5:89824794-89826468	A549	lung:	n/a	chr5:89825024-89825032
44	TBL1XR1	chr5:89825292-89826614	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:89703358..89707086-chr5:89823955..89827154,6	MCF-7	breast:
2	chr5:89825930..89827528-chr5:89867274..89868949,2	MCF-7	breast:
3	chr5:89825899..89828736-chr5:89905925..89909224,3	K562	blood:
4	chr5:89825541..89827508-chr5:89852797..89855537,2	MCF-7	breast:
5	chr5:89708413..89711602-chr5:89825612..89828655,3	K562	blood:
6	chr5:89825681..89827224-chr5:89844315..89846523,2	K562	blood:
7	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
8	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
9	chr5:89705290..89707109-chr5:89824364..89826854,3	MCF-7	breast:
10	chr5:89826199..89831045-chr5:89834037..89838315,7	K562	blood:
11	chr5:89825598..89829055-chr5:89851441..89854747,4	K562	blood:
12	chr5:89704960..89708059-chr5:89823269..89827144,6	K562	blood:
13	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
14	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
15	chr5:89703407..89707223-chr5:89822965..89826833,10	K562	blood:
16	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:
17	chr5:89734834..89736191-chr5:89825533..89826967,10	K562	blood:
18	chr5:89825636..89826384-chr5:89900047..89900941,2	K562	blood:

Variant related genes	Relation type
LYSMD3	TF binding region
ENSG00000255647	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000153140	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16868636	1.00[EUR][1000 genomes]
rs16868780	1.00[EUR][1000 genomes]
rs16868793	1.00[EUR][1000 genomes]
rs16868831	1.00[EUR][1000 genomes]
rs16868887	1.00[EUR][1000 genomes]
rs16868956	1.00[EUR][1000 genomes]
rs16868998	1.00[EUR][1000 genomes]
rs16869002	1.00[EUR][1000 genomes]
rs16869055	1.00[EUR][1000 genomes]
rs6452889	1.00[EUR][1000 genomes]
rs7721819	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking 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 target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89822600-89826600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:89823400-89826400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:89823600-89826400	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr5:89823600-89826400	Active TSS	GM12878-XiMat	blood
5	chr5:89823800-89826400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:89824000-89826400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr5:89824000-89826400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:89824000-89826600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr5:89824000-89826600	Active TSS	Aorta	Aorta
10	chr5:89824000-89826600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:89824000-89826600	Active TSS	HSMMtube	muscle
12	chr5:89824200-89826400	Active TSS	Brain Hippocampus Middle	brain
13	chr5:89824200-89826400	Active TSS	Fetal Stomach	stomach
14	chr5:89824200-89826600	Active TSS	Ovary	ovary
15	chr5:89824400-89826400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr5:89824400-89826400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:89824400-89826400	Active TSS	Psoas Muscle	Psoas
18	chr5:89824400-89826800	Active TSS	Thymus	Thymus
19	chr5:89824600-89826400	Active TSS	Stomach Mucosa	stomach
20	chr5:89824800-89826400	Active TSS	Brain Germinal Matrix	brain
21	chr5:89824800-89826400	Active TSS	Fetal Brain Female	brain
22	chr5:89825200-89826400	Active TSS	Primary T cells fromperipheralblood	blood
23	chr5:89825200-89826400	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr5:89825800-89826600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:89826000-89826400	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr5:89826000-89826400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr5:89826000-89826400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr5:89826000-89826400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:89826000-89826400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr5:89826000-89826400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr5:89826000-89826400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr5:89826000-89826400	Flanking Active TSS	HUVEC	blood vessel
33	chr5:89826000-89826600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:89826000-89826600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr5:89826000-89826600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr5:89826000-89826600	Flanking Active TSS	Dnd41	blood
37	chr5:89826000-89826600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr5:89826000-89826600	Flanking Active TSS	NHEK	skin
39	chr5:89826000-89826800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:89826000-89826800	Enhancers	Small Intestine	intestine
41	chr5:89826200-89826400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:89826200-89826400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:89826200-89826400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:89826200-89826400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr5:89826200-89826400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr5:89826200-89826400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:89826200-89826400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr5:89826200-89826400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:89826200-89826400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr5:89826200-89826400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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