Variant report

Variant	rs56893522
Chromosome Location	chr5:79553120-79553121
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	POLR2A	chr5:79551301-79553686	Hela-S3	cervix:	n/a	n/a
2	BHLHE40	chr5:79552956-79553713	K562	blood:	n/a	n/a
3	POLR2A	chr5:79552898-79553941	K562	blood:	n/a	n/a
4	POLR2A	chr5:79552857-79553695	HCT-116	colon:	n/a	n/a
5	CEBPB	chr5:79552940-79553728	K562	blood:	n/a	n/a
6	GTF2F1	chr5:79553042-79553839	K562	blood:	n/a	n/a
7	TBP	chr5:79552979-79553951	K562	blood:	n/a	n/a
8	MAFK	chr5:79553044-79553922	K562	blood:	n/a	chr5:79553434-79553443
9	MTA3	chr5:79552859-79553645	GM12878	blood:	n/a	n/a
10	TAF1	chr5:79552946-79553746	K562	blood:	n/a	n/a
11	POLR2A	chr5:79552934-79553921	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:79552993-79553503	HepG2	liver:	n/a	n/a
13	POLR2A	chr5:79552835-79553849	SK-N-MC	brain:	n/a	n/a
14	ATF3	chr5:79552928-79553657	K562	blood:	n/a	n/a
15	HMGN3	chr5:79553097-79553659	K562	blood:	n/a	n/a
16	EP300	chr5:79553065-79553825	ECC-1	luminal epithelium:	n/a	chr5:79553433-79553442
17	NR2F2	chr5:79552887-79553721	K562	blood:	n/a	n/a
18	ATF2	chr5:79552844-79553986	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr5:79552831-79554125	GM12878	blood:	n/a	n/a
20	E2F4	chr5:79553001-79553800	K562	blood:	n/a	chr5:79553602-79553616 chr5:79553605-79553612 chr5:79553604-79553613 chr5:79553605-79553612 chr5:79553605-79553612
21	HA-E2F1	chr5:79553010-79553868	MCF-7	breast:	n/a	chr5:79553602-79553616 chr5:79553605-79553612 chr5:79553604-79553613 chr5:79553605-79553612 chr5:79553605-79553612
22	TBP	chr5:79552945-79554029	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:79552908-79553808	HL-60	blood:	n/a	n/a
24	TAF7	chr5:79552859-79554094	H1-hESC	embryonic stem cell:	n/a	n/a
25	JUN	chr5:79553071-79553630	K562	blood:	n/a	chr5:79553433-79553442 chr5:79553432-79553441
26	EP300	chr5:79552991-79553976	K562	blood:	n/a	chr5:79553433-79553442
27	KAP1	chr5:79553045-79553678	U2OS	brain:	n/a	chr5:79553434-79553443
28	POLR2A	chr5:79553040-79553885	NB4	blood:	n/a	n/a
29	GATA1	chr5:79553098-79553658	PBDE	blood:	n/a	n/a
30	BHLHE40	chr5:79552956-79553528	GM12878	blood:	n/a	n/a
31	EP300	chr5:79552970-79553631	GM12878	blood:	n/a	chr5:79553433-79553442
32	ZMIZ1	chr5:79553020-79553929	K562	blood:	n/a	n/a
33	JUN	chr5:79552869-79554022	K562	blood:	n/a	chr5:79553433-79553442 chr5:79553432-79553441
34	MYC	chr5:79553002-79553734	K562	blood:	n/a	chr5:79553433-79553442
35	MAX	chr5:79552956-79553798	K562	blood:	n/a	chr5:79553433-79553442
36	MAX	chr5:79552957-79553835	NB4	blood:	n/a	chr5:79553433-79553442
37	CHD1	chr5:79551971-79554137	H1-hESC	embryonic stem cell:	n/a	n/a
38	CEBPB	chr5:79553001-79553260	HepG2	liver:	n/a	n/a
39	HEY1	chr5:79552939-79553746	K562	blood:	n/a	n/a
40	TAF1	chr5:79552944-79553710	K562	blood:	n/a	n/a
41	TBL1XR1	chr5:79553118-79553918	K562	blood:	n/a	n/a
42	MAZ	chr5:79552995-79553890	K562	blood:	n/a	chr5:79553433-79553442
43	POLR2A	chr5:79548149-79554758	H1-hESC	embryonic stem cell:	n/a	n/a
44	ARID3A	chr5:79553008-79553834	K562	blood:	n/a	n/a
45	MAFF	chr5:79553063-79553618	K562	blood:	n/a	n/a
46	POLR2A	chr5:79552931-79553708	ECC-1	luminal epithelium:	n/a	n/a
47	CHD2	chr5:79553092-79553672	K562	blood:	n/a	n/a
48	RCOR1	chr5:79553022-79553634	GM12878	blood:	n/a	n/a
49	EP300	chr5:79553002-79553627	GM12878	blood:	n/a	chr5:79553433-79553442
50	RAD21	chr5:79553010-79553817	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:79533016..79538413-chr5:79547668..79554494,9	MCF-7	breast:
2	chr5:79463693..79466330-chr5:79552172..79554632,2	MCF-7	breast:
3	chr5:79422174..79424739-chr5:79552545..79555468,2	K562	blood:
4	chr5:79471476..79473201-chr5:79552121..79553751,2	MCF-7	breast:
5	chr5:79463975..79466170-chr5:79552377..79554715,2	K562	blood:
6	chr5:79551714..79553387-chr5:79600959..79603373,2	MCF-7	breast:
7	chr5:79552295..79553879-chr5:79601080..79603735,2	K562	blood:
8	chr5:79552447..79554549-chr5:79614442..79617096,2	K562	blood:
9	chr5:79488184..79489719-chr5:79552242..79554634,2	K562	blood:
10	chr5:79423046..79425756-chr5:79550269..79553191,3	MCF-7	breast:
11	chr5:79528152..79532318-chr5:79552098..79554720,3	MCF-7	breast:
12	chr5:79551940..79553819-chr5:79583258..79585163,2	K562	blood:
13	chr5:79553026..79559305-chr5:79561133..79565052,9	K562	blood:
14	chr5:79550504..79553635-chr5:79702210..79704282,3	K562	blood:
15	chr5:79529349..79531030-chr5:79552067..79554937,3	K562	blood:
16	chr5:79462247..79466170-chr5:79549724..79555274,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPZ1-2	chr5:79552919-79554203	NONHSAT102395

Variant related genes	Relation type
SERINC5	TF binding region
ENSG00000251828	Chromatin interaction
ENSG00000251675	Chromatin interaction
ENSG00000164299	Chromatin interaction
ENSG00000249438	Chromatin interaction
ENSG00000239159	Chromatin interaction
ENSG00000039319	Chromatin interaction
ENSG00000164300	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16877662	0.82[AFR][1000 genomes]
rs1970862	0.85[ASN][1000 genomes]
rs6872359	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv3366910	chr5:79550846-79553244	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79549200-79553400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr5:79549200-79553400	Active TSS	Fetal Kidney	kidney
3	chr5:79549400-79553400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:79549800-79554600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:79550000-79553600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:79550000-79554200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr5:79550200-79553600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:79550200-79553600	Active TSS	Right Ventricle	heart
9	chr5:79550200-79554000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr5:79550400-79553600	Active TSS	Brain Angular Gyrus	brain
11	chr5:79550400-79553600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr5:79550400-79553800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:79550600-79553200	Active TSS	Brain Substantia Nigra	brain
14	chr5:79550800-79553600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:79550800-79554000	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr5:79551000-79553200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:79551200-79553400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:79552200-79553600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:79552200-79553800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr5:79552200-79553800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr5:79552400-79553600	Flanking Active TSS	Osteobl	bone
22	chr5:79552400-79553800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr5:79552400-79553800	Flanking Active TSS	Placenta	Placenta
24	chr5:79552400-79553800	Flanking Active TSS	Fetal Thymus	thymus
25	chr5:79552400-79553800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr5:79552400-79554000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr5:79552600-79553200	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr5:79552600-79553400	Weak transcription	Fetal Brain Male	brain
29	chr5:79552600-79553400	Enhancers	Placenta Amnion	Placenta Amnion
30	chr5:79552600-79553600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:79552600-79553600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr5:79552600-79553800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:79552600-79554000	Enhancers	Fetal Heart	heart
34	chr5:79552800-79553200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:79552800-79553200	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr5:79552800-79553200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:79552800-79553200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:79552800-79553200	Enhancers	Left Ventricle	heart
39	chr5:79552800-79553200	Enhancers	HMEC	breast
40	chr5:79552800-79553400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:79552800-79553400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:79552800-79553400	Weak transcription	Esophagus	oesophagus
43	chr5:79552800-79553400	Enhancers	Fetal Brain Female	brain
44	chr5:79552800-79553400	Enhancers	Fetal Muscle Leg	muscle
45	chr5:79552800-79553400	Enhancers	Fetal Stomach	stomach
46	chr5:79552800-79553400	Enhancers	Right Atrium	heart
47	chr5:79552800-79553400	Enhancers	HSMMtube	muscle
48	chr5:79552800-79553600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:79552800-79553600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr5:79552800-79553600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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