Variant report

Variant	rs616379
Chromosome Location	chr5:89826580-89826581
allele	G/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	CTCF	chr5:89826520-89826670	HPF	lung:	n/a	n/a
2	IRF1	chr5:89825195-89826614	K562	blood:	n/a	chr5:89826531-89826543 chr5:89826042-89826051
3	CTCF	chr5:89824880-89826659	SK-N-SH	brain:	n/a	chr5:89825024-89825032
4	EP300	chr5:89824639-89826652	K562	blood:	n/a	chr5:89826147-89826156 chr5:89825539-89825555
5	CTCF	chr5:89826460-89826610	AG10803	skin:	n/a	n/a
6	ZMIZ1	chr5:89824494-89826595	K562	blood:	n/a	n/a
7	JUN	chr5:89823293-89826982	K562	blood:	n/a	chr5:89826147-89826157 chr5:89826147-89826157 chr5:89826149-89826156 chr5:89826148-89826156 chr5:89826148-89826156 chr5:89826147-89826157
8	ARID3A	chr5:89825821-89826660	K562	blood:	n/a	n/a
9	RAD21	chr5:89824488-89826719	SK-N-SH	brain:	n/a	chr5:89825073-89825082 chr5:89825493-89825505
10	SMC3	chr5:89824820-89826683	SK-N-SH	brain:	n/a	n/a
11	CTCF	chr5:89826460-89826610	AG09319	gingival:	n/a	n/a
12	HCFC1	chr5:89824457-89826625	Hela-S3	cervix:	n/a	n/a
13	TBL1XR1	chr5:89825292-89826614	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:89703358..89707086-chr5:89823955..89827154,6	MCF-7	breast:
2	chr5:89825930..89827528-chr5:89867274..89868949,2	MCF-7	breast:
3	chr5:89825899..89828736-chr5:89905925..89909224,3	K562	blood:
4	chr5:89825541..89827508-chr5:89852797..89855537,2	MCF-7	breast:
5	chr5:89708413..89711602-chr5:89825612..89828655,3	K562	blood:
6	chr5:89825681..89827224-chr5:89844315..89846523,2	K562	blood:
7	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
8	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
9	chr5:89705290..89707109-chr5:89824364..89826854,3	MCF-7	breast:
10	chr5:89826199..89831045-chr5:89834037..89838315,7	K562	blood:
11	chr5:89825598..89829055-chr5:89851441..89854747,4	K562	blood:
12	chr5:89704960..89708059-chr5:89823269..89827144,6	K562	blood:
13	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
14	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
15	chr5:89703407..89707223-chr5:89822965..89826833,10	K562	blood:
16	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:
17	chr5:89734834..89736191-chr5:89825533..89826967,10	K562	blood:

Variant related genes	Relation type
LYSMD3	TF binding region
ENSG00000113356	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10473936	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1047787	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10514327	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10942597	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12655180	0.89[ASN][1000 genomes]
rs13182165	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185955	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673378	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1700510	0.85[EUR][1000 genomes]
rs1812737	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087840	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35407205	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3805483	0.88[ASN][1000 genomes]
rs474800	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs499148	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501640	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs552314	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs558809	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs587818	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603015	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603870	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618355	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs623761	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs648430	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666659	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67376567	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs688956	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6897910	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7716979	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7717423	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs616379	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89822600-89826600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:89824000-89826600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr5:89824000-89826600	Active TSS	Aorta	Aorta
4	chr5:89824000-89826600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:89824000-89826600	Active TSS	HSMMtube	muscle
6	chr5:89824200-89826600	Active TSS	Ovary	ovary
7	chr5:89824400-89826800	Active TSS	Thymus	Thymus
8	chr5:89825800-89826600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:89826000-89826600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:89826000-89826600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr5:89826000-89826600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr5:89826000-89826600	Flanking Active TSS	Dnd41	blood
13	chr5:89826000-89826600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr5:89826000-89826600	Flanking Active TSS	NHEK	skin
15	chr5:89826000-89826800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:89826000-89826800	Enhancers	Small Intestine	intestine
17	chr5:89826200-89826600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr5:89826200-89826600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:89826200-89826600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:89826200-89826600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr5:89826200-89826600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr5:89826200-89826600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr5:89826200-89826600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr5:89826200-89826600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr5:89826200-89826600	Enhancers	Primary B cells from peripheral blood	blood
26	chr5:89826200-89826600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:89826200-89826600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:89826200-89826600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:89826200-89826600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:89826200-89826600	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr5:89826200-89826600	Flanking Active TSS	Fetal Brain Male	brain
32	chr5:89826200-89826600	Enhancers	Fetal Heart	heart
33	chr5:89826200-89826600	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr5:89826200-89826600	Flanking Active TSS	Fetal Kidney	kidney
35	chr5:89826200-89826600	Flanking Active TSS	Fetal Lung	lung
36	chr5:89826200-89826600	Enhancers	Fetal Muscle Leg	muscle
37	chr5:89826200-89826600	Enhancers	Fetal Thymus	thymus
38	chr5:89826200-89826600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr5:89826200-89826600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr5:89826200-89826600	Flanking Active TSS	Hela-S3	cervix
41	chr5:89826200-89826600	Bivalent Enhancer	HepG2	liver
42	chr5:89826200-89826600	Flanking Active TSS	HMEC	breast
43	chr5:89826200-89826600	Enhancers	HSMM	muscle
44	chr5:89826200-89826600	Flanking Active TSS	NH-A	brain
45	chr5:89826200-89826600	Flanking Active TSS	NHLF	lung
46	chr5:89826200-89826800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr5:89826200-89826800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:89826200-89826800	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr5:89826200-89826800	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr5:89826200-89826800	Flanking Active TSS	Brain Anterior Caudate	brain

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