Variant report

Variant	rs599432
Chromosome Location	chr5:89843449-89843450
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	chr5:89703071..89706811-chr5:89843444..89846319,3	K562	blood:
2	chr5:89821919..89824561-chr5:89840686..89844146,3	MCF-7	breast:
3	chr5:89822535..89824744-chr5:89842428..89844021,2	K562	blood:
4	chr5:89705126..89706810-chr5:89842410..89844887,2	MCF-7	breast:
5	chr5:89842756..89845213-chr5:89939588..89942557,2	K562	blood:
6	chr5:89703142..89707771-chr5:89841561..89845408,5	K562	blood:
7	chr5:89768870..89770487-chr5:89842476..89844601,2	MCF-7	breast:
8	chr5:89841281..89844094-chr5:89853363..89855965,3	K562	blood:
9	chr5:89824636..89834797-chr5:89838005..89846568,18	MCF-7	breast:
10	chr5:89824246..89828197-chr5:89842395..89845815,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000255647	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10043564	0.85[JPT][hapmap]
rs10064606	0.86[JPT][hapmap]
rs10069050	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs11958484	0.85[JPT][hapmap]
rs12186867	0.85[JPT][hapmap]
rs12653924	1.00[JPT][hapmap]
rs149321	1.00[JPT][hapmap]
rs154568	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs154569	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs154570	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154572	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs154573	0.82[EUR][1000 genomes]
rs1553545	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs1673381	1.00[JPT][hapmap]
rs171790	0.87[EUR][1000 genomes]
rs2366772	1.00[JPT][hapmap]
rs2366775	0.95[JPT][hapmap]
rs250366	1.00[JPT][hapmap]
rs250377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs257847	1.00[JPT][hapmap]
rs257850	0.87[EUR][1000 genomes]
rs257851	0.88[EUR][1000 genomes]
rs2656957	0.87[EUR][1000 genomes]
rs27196	1.00[JPT][hapmap]
rs27197	1.00[JPT][hapmap]
rs27201	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs37238	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs37239	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs37240	0.83[EUR][1000 genomes]
rs42467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs43149	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4588621	1.00[JPT][hapmap]
rs491082	0.87[EUR][1000 genomes]
rs5028525	1.00[JPT][hapmap]
rs511393	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs526806	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs556894	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59159252	0.92[ASN][1000 genomes]
rs594990	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs625135	0.96[CEU][hapmap];0.83[JPT][hapmap]
rs649449	1.00[JPT][hapmap]
rs656679	1.00[JPT][hapmap]
rs679568	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs6892132	1.00[JPT][hapmap]
rs810974	0.87[EUR][1000 genomes]
rs908818	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs599432	LYSMD3	cis	normal skin	skin_eQTL
rs599432	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89839400-89844200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:89840400-89845200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:89840800-89845800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:89842200-89844000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:89842200-89844200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr5:89842200-89844400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:89842200-89844600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:89842200-89844800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr5:89842400-89843600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:89842600-89843800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:89842800-89844400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:89842800-89844400	Enhancers	HepG2	liver
13	chr5:89842800-89844600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr5:89843000-89843600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr5:89843000-89844000	Bivalent/Poised TSS	A549	lung
16	chr5:89843000-89844200	Enhancers	Brain Cingulate Gyrus	brain
17	chr5:89843000-89844400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr5:89843000-89844400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:89843000-89844400	Enhancers	Hela-S3	cervix
20	chr5:89843000-89844600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:89843200-89843600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:89843200-89844000	Enhancers	K562	blood
23	chr5:89843200-89844400	Enhancers	Brain Substantia Nigra	brain
24	chr5:89843400-89843800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:89843400-89844200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:89843400-89849600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr5:89843400-89852800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:89843400-89853200	Weak transcription	Brain Anterior Caudate	brain

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