Variant report

Variant	rs603870
Chromosome Location	chr5:89825210-89825211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89703358..89707086-chr5:89823955..89827154,6	MCF-7	breast:
2	chr5:89705255..89705991-chr5:89825165..89825777,2	NB4	blood:
3	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
4	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
5	chr5:89705290..89707109-chr5:89824364..89826854,3	MCF-7	breast:
6	chr5:89704960..89708059-chr5:89823269..89827144,6	K562	blood:
7	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
8	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
9	chr5:89703407..89707223-chr5:89822965..89826833,10	K562	blood:
10	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000176055	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	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1047787	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10514327	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10942597	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12655180	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13182165	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185955	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673378	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1700510	0.87[EUR][1000 genomes]
rs1812737	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087840	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35407205	0.88[ASN][1000 genomes]
rs3805483	0.88[ASN][1000 genomes]
rs474800	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs499148	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501640	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs552314	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs558809	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs587818	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603015	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616379	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618355	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs623761	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs648430	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666659	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67376567	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs688956	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6897910	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7716979	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7717423	0.89[AMR][1000 genomes];0.97[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
rs603870	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89822600-89826600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:89823200-89826200	Active TSS	Right Atrium	heart
3	chr5:89823200-89826200	Active TSS	NHLF	lung
4	chr5:89823400-89826400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:89823600-89826000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:89823600-89826200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr5:89823600-89826200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:89823600-89826200	Active TSS	Fetal Intestine Large	intestine
9	chr5:89823600-89826200	Active TSS	K562	blood
10	chr5:89823600-89826200	Active TSS	NH-A	brain
11	chr5:89823600-89826200	Active TSS	NHDF-Ad	bronchial
12	chr5:89823600-89826400	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr5:89823600-89826400	Active TSS	GM12878-XiMat	blood
14	chr5:89823800-89826200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr5:89823800-89826200	Active TSS	HMEC	breast
16	chr5:89823800-89826400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:89824000-89826000	Active TSS	NHEK	skin
18	chr5:89824000-89826200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr5:89824000-89826200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:89824000-89826200	Active TSS	Colonic Mucosa	Colon
21	chr5:89824000-89826200	Active TSS	Colon Smooth Muscle	Colon
22	chr5:89824000-89826200	Active TSS	Right Ventricle	heart
23	chr5:89824000-89826400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr5:89824000-89826400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:89824000-89826600	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr5:89824000-89826600	Active TSS	Aorta	Aorta
27	chr5:89824000-89826600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr5:89824000-89826600	Active TSS	HSMMtube	muscle
29	chr5:89824200-89826000	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr5:89824200-89826000	Active TSS	Placenta	Placenta
31	chr5:89824200-89826000	Active TSS	Placenta Amnion	Placenta Amnion
32	chr5:89824200-89826200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:89824200-89826200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:89824200-89826200	Active TSS	Brain Angular Gyrus	brain
35	chr5:89824200-89826200	Active TSS	Brain Anterior Caudate	brain
36	chr5:89824200-89826200	Active TSS	Fetal Intestine Small	intestine
37	chr5:89824200-89826200	Active TSS	Fetal Muscle Trunk	muscle
38	chr5:89824200-89826200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr5:89824200-89826200	Active TSS	HSMM	muscle
40	chr5:89824200-89826400	Active TSS	Brain Hippocampus Middle	brain
41	chr5:89824200-89826400	Active TSS	Fetal Stomach	stomach
42	chr5:89824200-89826600	Active TSS	Ovary	ovary
43	chr5:89824400-89825400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:89824400-89826000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:89824400-89826000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:89824400-89826000	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr5:89824400-89826000	Active TSS	Gastric	stomach
48	chr5:89824400-89826000	Active TSS	Lung	lung
49	chr5:89824400-89826200	Active TSS	H9 Cell Line	embryonic stem cell
50	chr5:89824400-89826200	Active TSS	iPS-15b Cell Line	embryonic stem cell

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