Variant report

Variant	rs3087840
Chromosome Location	chr5:89812676-89812677
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89812385..89814878-chr5:89823599..89825330,3	MCF-7	breast:
2	chr5:89810981..89813583-chr5:89821226..89822873,2	MCF-7	breast:
3	chr5:89795388..89799823-chr5:89809630..89813266,4	K562	blood:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10462342	0.80[ASN][1000 genomes]
rs10473936	0.89[EUR][1000 genomes]
rs1047787	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514327	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942597	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12655180	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13182165	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13185955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1673378	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1700510	0.84[EUR][1000 genomes]
rs1812737	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35407205	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3805483	0.90[ASN][1000 genomes]
rs474800	0.82[EUR][1000 genomes]
rs499148	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs501640	0.92[EUR][1000 genomes]
rs552314	0.82[EUR][1000 genomes]
rs558809	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs587818	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs603015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs603870	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs616379	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs618355	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs623761	0.82[EUR][1000 genomes]
rs648430	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs666659	0.87[EUR][1000 genomes]
rs67376567	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs688956	0.82[EUR][1000 genomes]
rs6897910	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7716979	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7717423	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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
rs3087840	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89771600-89814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:89773800-89816000	Weak transcription	HepG2	liver
3	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:89774000-89814600	Weak transcription	Dnd41	blood
5	chr5:89774400-89814600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:89783800-89813400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:89784800-89814600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:89785400-89814600	Weak transcription	NHLF	lung
10	chr5:89791400-89814600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:89791600-89813800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:89791600-89814600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:89793800-89823400	Weak transcription	Hela-S3	cervix
14	chr5:89797600-89814600	Weak transcription	Adipose Nuclei	Adipose
15	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
16	chr5:89798000-89814600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:89799600-89817200	Weak transcription	NHDF-Ad	bronchial
18	chr5:89799800-89814600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:89800000-89814400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:89800000-89814600	Weak transcription	NHEK	skin
21	chr5:89800800-89814600	Weak transcription	HMEC	breast
22	chr5:89801000-89813600	Weak transcription	NH-A	brain
23	chr5:89801000-89814600	Weak transcription	HUVEC	blood vessel
24	chr5:89802600-89824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:89803200-89817600	Weak transcription	Small Intestine	intestine
26	chr5:89804000-89813400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:89804000-89816400	Weak transcription	Thymus	Thymus
28	chr5:89804800-89814600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:89805600-89819800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:89805600-89823200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:89805800-89819800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:89806000-89814800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:89806400-89818200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:89808000-89814000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:89808200-89814400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:89808600-89814400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:89808600-89814600	Weak transcription	Osteobl	bone
38	chr5:89808800-89814200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:89808800-89814600	Weak transcription	Fetal Muscle Leg	muscle
40	chr5:89808800-89814600	Weak transcription	Placenta	Placenta
41	chr5:89808800-89814600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:89808800-89816000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr5:89808800-89822000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr5:89809000-89813600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:89809000-89814400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:89809000-89814400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:89809000-89814400	Weak transcription	Fetal Thymus	thymus
48	chr5:89809000-89814600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:89809000-89814600	Weak transcription	Brain Substantia Nigra	brain
50	chr5:89809000-89814800	Weak transcription	Fetal Brain Female	brain

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