Variant report

Variant	rs4479864
Chromosome Location	chr5:95414555-95414556
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	PBX3	chr5:95414202-95414701	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr5:95414154-95415313	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr5:95414230-95414716	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr5:95414182-95415359	SK-N-SH	brain:	n/a	n/a
5	EP300	chr5:95414236-95414578	SK-N-SH_RA	brain:	n/a	n/a
6	TCF12	chr5:95414270-95415342	SK-N-SH	brain:	n/a	n/a
7	EP300	chr5:95414172-95415384	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
MIR583	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10056771	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10079268	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10085034	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11740207	0.86[EUR][1000 genomes]
rs11949461	0.86[EUR][1000 genomes]
rs11951463	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11956456	0.86[EUR][1000 genomes]
rs11960219	0.86[EUR][1000 genomes]
rs13155375	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13172783	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13186419	0.87[EUR][1000 genomes]
rs1389827	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1870270	0.88[EUR][1000 genomes]
rs2067498	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4077350	0.83[EUR][1000 genomes]
rs4128178	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4270717	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4367316	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4416625	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4513721	0.86[EUR][1000 genomes]
rs4869256	0.95[EUR][1000 genomes]
rs4869258	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4869259	0.86[EUR][1000 genomes]
rs4869260	0.86[EUR][1000 genomes]
rs4869264	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4869266	0.84[EUR][1000 genomes]
rs4998057	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6556899	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6556900	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs66683317	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6866723	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6873504	0.86[EUR][1000 genomes]
rs6879658	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6879847	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6884999	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6886983	0.84[EUR][1000 genomes]
rs6889697	0.86[EUR][1000 genomes]
rs6894768	0.86[EUR][1000 genomes]
rs6895121	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6895146	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7341111	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7700425	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7702346	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7702646	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7710337	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7715650	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7717351	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7734224	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7734985	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9314163	0.89[EUR][1000 genomes]
rs9314164	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9314165	0.86[EUR][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	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv823146	chr5:95300912-95453557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	esv2757121	chr5:95304236-95539536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	esv34203	chr5:95310985-95452324	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv522097	chr5:95347786-95425199	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv522465	chr5:95347786-95425199	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95401600-95416400	Weak transcription	Psoas Muscle	Psoas
2	chr5:95402600-95423800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:95404400-95416800	Weak transcription	Aorta	Aorta
4	chr5:95406800-95414800	Weak transcription	NHLF	lung
5	chr5:95408200-95416600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:95409600-95416400	Weak transcription	Gastric	stomach
7	chr5:95410800-95416800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:95410800-95420400	Weak transcription	Stomach Mucosa	stomach
9	chr5:95412000-95420800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:95412200-95417000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:95412400-95416400	Weak transcription	HepG2	liver
12	chr5:95413000-95415400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:95413000-95416800	Enhancers	NHEK	skin
14	chr5:95413000-95417000	Enhancers	A549	lung
15	chr5:95413000-95417600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:95413200-95415600	Enhancers	Osteobl	bone
17	chr5:95413200-95417400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:95413200-95417400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:95413200-95417400	Enhancers	Hela-S3	cervix
20	chr5:95413200-95417600	Enhancers	HMEC	breast
21	chr5:95413200-95419800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:95413400-95414600	Enhancers	Fetal Heart	heart
23	chr5:95413400-95416400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:95413400-95418200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:95413600-95417000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:95413800-95416000	Enhancers	NH-A	brain
27	chr5:95413800-95417600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:95414200-95414800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:95414200-95415600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:95414200-95417200	Enhancers	NHDF-Ad	bronchial
31	chr5:95414400-95414600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr5:95414400-95415000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:95414400-95415200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:95414400-95415400	Enhancers	HSMMtube	muscle
35	chr5:95414400-95417200	Enhancers	HSMM	muscle
36	chr5:95414400-95417600	Enhancers	HUVEC	blood vessel

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