Variant report

Variant	rs6452410
Chromosome Location	chr5:80747220-80747221
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	TEAD4	chr5:80746657-80747261	HepG2	liver:	n/a	n/a
2	FOXA1	chr5:80746388-80747265	HepG2	liver:	n/a	n/a
3	NFIC	chr5:80746719-80747253	HepG2	liver:	n/a	n/a
4	SP1	chr5:80746803-80747225	HepG2	liver:	n/a	n/a
5	CEBPB	chr5:80746811-80747224	HepG2	liver:	n/a	chr5:80747018-80747029

Variant related genes	Relation type
SSBP2	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10035291	0.82[ASN][1000 genomes]
rs10036712	0.83[ASN][1000 genomes]
rs10041030	0.89[ASN][1000 genomes]
rs10042303	0.84[ASN][1000 genomes]
rs10043164	0.81[ASN][1000 genomes]
rs10056711	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068144	0.88[ASN][1000 genomes]
rs10075648	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474031	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942266	0.94[ASN][1000 genomes]
rs11739075	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12697705	0.87[ASN][1000 genomes]
rs13159500	0.89[ASN][1000 genomes]
rs13171682	0.98[ASN][1000 genomes]
rs1541830	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2162973	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396170	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34150522	0.81[ASN][1000 genomes]
rs34699788	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35224297	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452407	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452411	0.85[ASN][1000 genomes]
rs6452412	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452414	0.83[ASN][1000 genomes]
rs6452415	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866156	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866741	0.84[ASN][1000 genomes]
rs6868422	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868748	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872775	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872793	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874237	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6877102	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878037	0.80[ASN][1000 genomes]
rs6883488	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887937	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897189	0.89[ASN][1000 genomes]
rs7711020	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719373	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725126	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733938	0.81[ASN][1000 genomes]
rs9293275	0.85[ASN][1000 genomes]
rs9596	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964102	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1028498	chr5:80712364-80860430	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80703200-80779200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:80704400-80747600	Weak transcription	Placenta	Placenta
3	chr5:80707400-80748400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:80709200-80755200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:80713600-80769200	Weak transcription	Esophagus	oesophagus
6	chr5:80716200-80767800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:80716800-80768400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:80717200-80769200	Weak transcription	Right Ventricle	heart
9	chr5:80718000-80768800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:80718400-80752600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:80718400-80754800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:80718400-80755000	Weak transcription	GM12878-XiMat	blood
13	chr5:80719000-80769200	Weak transcription	HSMMtube	muscle
14	chr5:80722000-80754800	Weak transcription	HSMM	muscle
15	chr5:80722400-80754800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:80722400-80755200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:80722400-80768800	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:80722400-80768800	Weak transcription	Fetal Brain Female	brain
19	chr5:80722600-80748600	Weak transcription	Ovary	ovary
20	chr5:80722600-80767600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:80722600-80768000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:80722600-80768200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:80722600-80769000	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:80722600-80769000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:80722600-80769000	Weak transcription	Fetal Brain Male	brain
26	chr5:80722600-80769000	Weak transcription	Psoas Muscle	Psoas
27	chr5:80722600-80769200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:80722800-80747800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:80722800-80748400	Weak transcription	Fetal Lung	lung
30	chr5:80722800-80755200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:80724000-80748400	Weak transcription	Fetal Muscle Leg	muscle
32	chr5:80725200-80748000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:80725400-80755200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:80729600-80769200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:80729800-80769200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:80730600-80767800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:80731400-80749000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr5:80731400-80768800	Weak transcription	Fetal Kidney	kidney
39	chr5:80731800-80769200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:80732000-80748200	Weak transcription	Thymus	Thymus
41	chr5:80733600-80756000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:80734400-80748400	Weak transcription	K562	blood
43	chr5:80735400-80778600	Weak transcription	Aorta	Aorta
44	chr5:80736000-80771200	Weak transcription	NHDF-Ad	bronchial
45	chr5:80736400-80768800	Weak transcription	Fetal Intestine Large	intestine
46	chr5:80736600-80747800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr5:80736800-80748400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:80737600-80748000	Weak transcription	Primary T cells from cord blood	blood
49	chr5:80738200-80768400	Weak transcription	Brain Germinal Matrix	brain
50	chr5:80739200-80769000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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