Variant report

Variant	rs55896641
Chromosome Location	chr5:79928011-79928012
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	TBP	chr5:79927604-79928086	HepG2	liver:	n/a	n/a
2	SMC3	chr5:79927557-79928189	HepG2	liver:	n/a	n/a
3	EP300	chr5:79927675-79928144	HepG2	liver:	n/a	chr5:79927731-79927741 chr5:79927676-79927690
4	POLR2A	chr5:79927172-79929435	K562	blood:	n/a	n/a
5	HEY1	chr5:79927899-79928080	HepG2	liver:	n/a	n/a
6	MYBL2	chr5:79927550-79928171	HepG2	liver:	n/a	n/a
7	FOXA2	chr5:79927660-79928086	HepG2	liver:	n/a	chr5:79927728-79927740
8	NFIC	chr5:79927628-79928120	HepG2	liver:	n/a	n/a
9	HDAC2	chr5:79927605-79928104	HepG2	liver:	n/a	chr5:79928015-79928029
10	ARID3A	chr5:79927513-79928341	HepG2	liver:	n/a	n/a
11	SP1	chr5:79927590-79928183	HepG2	liver:	n/a	n/a
12	RAD21	chr5:79927495-79928160	HepG2	liver:	n/a	n/a
13	HNF4G	chr5:79927703-79928066	HepG2	liver:	n/a	chr5:79927982-79927997 chr5:79927982-79927996 chr5:79927878-79927893
14	FOXA1	chr5:79927575-79928155	HepG2	liver:	n/a	chr5:79927728-79927740
15	HNF4A	chr5:79927749-79928108	HepG2	liver:	n/a	chr5:79927879-79927894 chr5:79927982-79927997 chr5:79927982-79927996
16	TEAD4	chr5:79927600-79928349	HepG2	liver:	n/a	n/a
17	TCF7L2	chr5:79927670-79928199	HepG2	liver:	n/a	n/a
18	CREB1	chr5:79927324-79928052	HepG2	liver:	n/a	n/a
19	HNF4A	chr5:79927695-79928014	HepG2	liver:	n/a	chr5:79927879-79927894 chr5:79927982-79927997 chr5:79927982-79927996
20	FOXA1	chr5:79927606-79928070	HepG2	liver:	n/a	chr5:79927728-79927740
21	HDAC2	chr5:79927653-79928025	HepG2	liver:	n/a	n/a
22	CEBPB	chr5:79927827-79928236	HepG2	liver:	n/a	chr5:79928143-79928156 chr5:79928144-79928155
23	FOXA1	chr5:79927538-79928189	HepG2	liver:	n/a	chr5:79927728-79927740
24	EP300	chr5:79927607-79928178	HepG2	liver:	n/a	chr5:79927731-79927741 chr5:79927676-79927690
25	JUND	chr5:79927519-79928232	HepG2	liver:	n/a	n/a
26	POLR2A	chr5:79928011-79928059	Hela-S3	cervix:	n/a	n/a
27	MYBL2	chr5:79927413-79928149	HepG2	liver:	n/a	n/a
28	FOXA1	chr5:79927532-79928139	HepG2	liver:	n/a	chr5:79927728-79927740

Variant related genes	Relation type
ENSG00000249655	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16877918	1.00[ASN][1000 genomes]
rs17263489	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35709834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56212706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151630	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765545	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72765546	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765547	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765548	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765549	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765552	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765560	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72765561	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72765566	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765582	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79906600-79949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:79912000-79938000	Weak transcription	Brain Anterior Caudate	brain
3	chr5:79912200-79928600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:79912200-79948000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:79913200-79949000	Weak transcription	Spleen	Spleen
6	chr5:79913600-79949400	Weak transcription	Esophagus	oesophagus
7	chr5:79914200-79949400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:79915400-79949200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:79915600-79934600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:79916200-79936200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:79916400-79932800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:79916600-79949400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:79917000-79935800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:79919000-79936200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:79919600-79949200	Weak transcription	Colonic Mucosa	Colon
16	chr5:79919600-79949800	Weak transcription	Pancreas	Pancrea
17	chr5:79919800-79934400	Weak transcription	Ovary	ovary
18	chr5:79919800-79949000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:79920200-79935600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:79920200-79936400	Weak transcription	NHLF	lung
21	chr5:79920200-79949000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:79920200-79949000	Weak transcription	Stomach Mucosa	stomach
23	chr5:79920600-79935200	Weak transcription	Fetal Kidney	kidney
24	chr5:79921400-79935800	Weak transcription	Brain Substantia Nigra	brain
25	chr5:79921800-79936800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:79923000-79936600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:79923600-79933400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:79923600-79939600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr5:79923600-79949800	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:79923800-79936200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:79924000-79934400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:79924000-79934800	Weak transcription	Fetal Brain Female	brain
33	chr5:79924000-79936600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:79924200-79936200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:79924200-79936600	Weak transcription	Lung	lung
36	chr5:79924200-79949200	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:79924200-79949400	Weak transcription	Right Ventricle	heart
38	chr5:79924200-79949800	Weak transcription	Left Ventricle	heart
39	chr5:79924400-79945800	Strong transcription	Dnd41	blood
40	chr5:79924400-79949200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:79924600-79940000	Weak transcription	Fetal Heart	heart
42	chr5:79924800-79943000	Weak transcription	Brain Germinal Matrix	brain
43	chr5:79925000-79928200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:79925000-79938600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:79925000-79946200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:79925200-79930200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:79925200-79934000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr5:79925200-79939400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:79925200-79945600	Strong transcription	Fetal Thymus	thymus
50	chr5:79925200-79945800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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