Variant report

Variant	rs10064606
Chromosome Location	chr5:89952979-89952980
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89767160..89772090-chr5:89951866..89955351,7	K562	blood:
2	chr5:89952329..89954940-chr5:90078278..90080126,2	K562	blood:
3	chr5:89950917..89953812-chr5:89965739..89968417,3	K562	blood:
4	chr5:89950925..89957089-chr5:90674771..90680308,6	K562	blood:
5	chr5:89951486..89954210-chr5:89956379..89958966,2	MCF-7	breast:
6	chr5:89768742..89770418-chr5:89952039..89954929,2	K562	blood:
7	chr5:89824307..89827055-chr5:89951973..89954054,2	K562	blood:
8	chr5:89908142..89911258-chr5:89951635..89955571,4	K562	blood:
9	chr5:89908957..89911258-chr5:89952267..89954603,2	K562	blood:
10	chr5:89702933..89707863-chr5:89951683..89955435,5	K562	blood:
11	chr5:89899238..89902193-chr5:89950994..89956361,5	K562	blood:
12	chr5:89948021..89949895-chr5:89950501..89953146,2	MCF-7	breast:
13	chr5:89702933..89707555-chr5:89951683..89956853,5	K562	blood:
14	chr5:89899642..89902183-chr5:89950994..89955309,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000255647	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000113356	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10035335	0.85[EUR][1000 genomes]
rs10037067	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs10040165	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs10043564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs10942604	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs11958484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12186867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12653924	0.80[CHB][hapmap]
rs1474119	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs1474120	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs149321	0.83[JPT][hapmap]
rs1568308	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1673381	0.84[JPT][hapmap]
rs16868980	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs16868999	1.00[CEU][hapmap];0.96[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs16869010	1.00[CEU][hapmap];0.96[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs16869042	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs16876822	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs171630	0.85[EUR][1000 genomes]
rs2366772	0.82[JPT][hapmap]
rs2366926	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs250366	0.84[JPT][hapmap]
rs250369	0.86[EUR][1000 genomes]
rs257847	0.82[JPT][hapmap]
rs27196	0.82[JPT][hapmap]
rs27197	0.83[JPT][hapmap]
rs28796004	0.86[EUR][1000 genomes]
rs4588621	0.83[JPT][hapmap]
rs4916683	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4916685	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4916808	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5028525	0.83[JPT][hapmap]
rs55835641	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56255871	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56369423	0.82[EUR][1000 genomes]
rs599432	0.86[JPT][hapmap]
rs62375083	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62375094	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62375106	0.88[EUR][1000 genomes]
rs649449	0.83[JPT][hapmap]
rs656679	0.83[JPT][hapmap]
rs6861067	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6880239	1.00[CEU][hapmap];0.96[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6892132	0.83[JPT][hapmap]
rs7716829	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs908818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9283789	0.88[EUR][1000 genomes]
rs9293549	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs970319	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv933161	chr5:89939500-89954066	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv1029970	chr5:89940489-89986831	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv1032225	chr5:89940489-89999954	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv1025391	chr5:89943364-89995164	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv537805	chr5:89943364-89995164	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10064606	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89936800-89994200	Weak transcription	Brain Germinal Matrix	brain
2	chr5:89941400-89957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:89941600-89954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:89941800-89957600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:89944800-89956600	Weak transcription	Fetal Brain Male	brain
6	chr5:89948000-89955400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:89948000-89955800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:89949600-89954600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:89949600-89964000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:89950200-89953200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:89950200-89953800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:89950200-89954400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:89950200-89981600	Weak transcription	Fetal Brain Female	brain
14	chr5:89950400-89956600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:89950400-90033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:89950800-89964000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:89950800-89973800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:89951800-89956200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:89952400-89953000	Genic enhancers	K562	blood
20	chr5:89952400-89957200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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