Variant report

Variant	rs11958484
Chromosome Location	chr5:89954184-89954185
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 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	chr5:89950925..89957089-chr5:90674771..90680308,6	K562	blood:
4	chr5:89951486..89954210-chr5:89956379..89958966,2	MCF-7	breast:
5	chr5:89768742..89770418-chr5:89952039..89954929,2	K562	blood:
6	chr5:89953449..89955208-chr5:90677507..90679070,2	K562	blood:
7	chr5:89908142..89911258-chr5:89951635..89955571,4	K562	blood:
8	chr5:89908957..89911258-chr5:89952267..89954603,2	K562	blood:
9	chr5:89702933..89707863-chr5:89951683..89955435,5	K562	blood:
10	chr5:89899238..89902193-chr5:89950994..89956361,5	K562	blood:
11	chr5:89702933..89707555-chr5:89951683..89956853,5	K562	blood:
12	chr5:89899642..89902183-chr5:89950994..89955309,3	K562	blood:

No data

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

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10035335	0.85[EUR][1000 genomes]
rs10037067	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs10040165	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs10043564	0.94[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10064606	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]
rs10942604	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs12186867	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1474119	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs1474120	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs149321	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs1568308	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap]
rs1673381	0.83[JPT][hapmap]
rs16868980	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs16868999	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs16869010	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs16869042	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap]
rs16876822	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs171630	0.85[EUR][1000 genomes]
rs2366772	0.81[JPT][hapmap]
rs2366926	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs250366	0.83[JPT][hapmap]
rs250369	0.86[EUR][1000 genomes]
rs257847	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs27196	0.80[JPT][hapmap]
rs27197	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs28796004	0.86[EUR][1000 genomes]
rs4588621	0.82[JPT][hapmap]
rs4916683	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4916685	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4916808	0.90[EUR][1000 genomes]
rs5028525	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs55835641	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56255871	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56369423	0.82[EUR][1000 genomes]
rs599432	0.85[JPT][hapmap]
rs62375083	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62375094	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62375106	0.88[EUR][1000 genomes]
rs649449	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs656679	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs6861067	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6880239	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6892132	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs7716829	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs908818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9283789	0.88[EUR][1000 genomes]
rs9293549	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs970319	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
7	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
8	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
9	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11958484	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL
rs11958484	GPR98	cis	cerebellum	SCAN

Chromatin state (count:19 , 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	chr5:89950200-89954400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:89950200-89981600	Weak transcription	Fetal Brain Female	brain
12	chr5:89950400-89956600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:89950400-90033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:89950800-89964000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:89950800-89973800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:89951800-89956200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:89952400-89957200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:89953400-89954400	Transcr. at gene 5' and 3'	K562	blood
19	chr5:89953800-89955400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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