Variant report

Variant	rs3805478
Chromosome Location	chr5:89772357-89772358
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr5:89772071-89772568	K562	blood:	n/a	chr5:89772452-89772463
2	CTCF	chr5:89772320-89772470	GM12873	blood:	n/a	n/a
3	ARID3A	chr5:89772341-89772608	K562	blood:	n/a	n/a
4	CTCF	chr5:89772337-89772620	K562	blood:	n/a	n/a
5	CTCF	chr5:89772347-89772387	GM12878	blood:	n/a	n/a
6	MYC	chr5:89772145-89772528	K562	blood:	n/a	n/a
7	MAFF	chr5:89771982-89772493	K562	blood:	n/a	n/a
8	MAFK	chr5:89771943-89772555	K562	blood:	n/a	chr5:89772436-89772447 chr5:89772436-89772447
9	EP300	chr5:89772213-89772442	K562	blood:	n/a	chr5:89772233-89772247
10	CTCF	chr5:89772280-89772430	GM12878	blood:	n/a	n/a
11	RCOR1	chr5:89771952-89772466	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89771966..89773493-chr5:89774062..89776128,2	MCF-7	breast:
2	chr5:89770745..89773686-chr5:89789440..89792433,3	K562	blood:
3	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
4	chr5:89702524..89708084-chr5:89764247..89773389,22	K562	blood:
5	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:
6	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
7	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
8	chr5:89770310..89772686-chr5:89934294..89936742,2	K562	blood:

No data

Variant related genes	Relation type
MBLAC2	TF binding region
ENSG00000153140	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10041220	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10043702	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10214167	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10473934	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs10942593	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10942594	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11953207	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11956418	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12516555	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13436287	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2303801	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28728101	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28815472	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34397682	0.86[EUR][1000 genomes]
rs3763070	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3763072	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59742368	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61610742	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6864062	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6867534	0.91[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6872360	0.87[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6889253	0.87[EUR][1000 genomes]
rs6889947	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs6890115	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs7729481	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7730433	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7732363	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv518131	chr5:89748142-89781594	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
9	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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89768800-89773200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr5:89768800-89773400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:89769000-89772400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:89769200-89772400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr5:89769200-89773800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr5:89770600-89773400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:89771200-89772400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:89771200-89772600	Enhancers	Brain Anterior Caudate	brain
9	chr5:89771200-89772800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:89771200-89772800	Weak transcription	Liver	Liver
11	chr5:89771200-89772800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:89771200-89773000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:89771200-89773000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr5:89771200-89773000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:89771200-89773000	Enhancers	Brain Substantia Nigra	brain
16	chr5:89771200-89773400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr5:89771200-89773400	Weak transcription	Adipose Nuclei	Adipose
18	chr5:89771200-89773400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:89771200-89773800	Enhancers	HepG2	liver
20	chr5:89771200-89784000	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:89771200-89788600	Weak transcription	Psoas Muscle	Psoas
22	chr5:89771200-89796200	Weak transcription	Fetal Intestine Small	intestine
23	chr5:89771400-89772400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:89771600-89772400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:89771600-89772800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:89771600-89772800	Enhancers	Dnd41	blood
27	chr5:89771600-89773000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:89771600-89773000	Weak transcription	NHLF	lung
29	chr5:89771600-89773400	Weak transcription	HMEC	breast
30	chr5:89771600-89773800	Weak transcription	NHDF-Ad	bronchial
31	chr5:89771600-89774000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:89771600-89774000	Enhancers	HUVEC	blood vessel
33	chr5:89771600-89775200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:89771600-89775400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:89771600-89775600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:89771600-89798800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:89771600-89814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:89771800-89773000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:89771800-89773800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:89771800-89774200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:89772000-89772600	Enhancers	A549	lung
42	chr5:89772000-89772800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:89772000-89772800	Weak transcription	Brain Angular Gyrus	brain
44	chr5:89772000-89773200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr5:89772000-89773400	Transcr. at gene 5' and 3'	K562	blood
46	chr5:89772000-89773800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr5:89772000-89774000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr5:89772000-89774000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr5:89772000-89774200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr5:89772200-89772400	Active TSS	ES-I3 Cell Line	embryonic stem cell

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