Variant report

Variant	rs2438361
Chromosome Location	chr5:90090437-90090438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90087371..90091009-chr5:90095949..90098739,3	K562	blood:
2	chr5:90088753..90091420-chr5:90094556..90098739,3	K562	blood:
3	chr5:89769110..89772331-chr5:90086907..90091587,4	K562	blood:

Variant related genes	Relation type
ENSG00000176055	Chromatin interaction
ENSG00000113356	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10514337	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs11956622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12655163	0.91[ASN][1000 genomes]
rs12655900	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12657829	0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs16869112	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs16869117	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs16869133	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs16869139	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16869140	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16869151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16869163	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1983366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2203823	0.88[CHB][hapmap]
rs2244265	0.90[AFR][1000 genomes]
rs2366932	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2438339	0.88[CHB][hapmap]
rs2438352	0.80[JPT][hapmap]
rs2438366	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2438375	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2438377	0.88[ASN][1000 genomes]
rs2438379	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2438380	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2443076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2443084	0.91[ASN][1000 genomes]
rs3107223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3763073	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6893549	0.82[CEU][hapmap]
rs7735712	0.82[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs879571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][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	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
5	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv934323	chr5:89968158-90111853	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1031718	chr5:89999033-90099868	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv968840	chr5:90089029-90097179	Enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90051800-90105000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:90061200-90090800	Weak transcription	Brain Anterior Caudate	brain
3	chr5:90082800-90090600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:90086200-90092200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:90086600-90090600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:90086600-90091800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:90087000-90091800	Strong transcription	Fetal Brain Female	brain
8	chr5:90087400-90090800	ZNF genes & repeats	K562	blood
9	chr5:90088600-90092200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr5:90089000-90090600	Weak transcription	Brain Germinal Matrix	brain
11	chr5:90089200-90091800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
12	chr5:90089200-90092400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr5:90089400-90092000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:90089600-90090600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:90089600-90091000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
16	chr5:90089800-90091200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr5:90089800-90092400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:90089800-90092600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:90090000-90092200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr5:90090200-90091400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
21	chr5:90090200-90092400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:90090400-90090600	ZNF genes & repeats	Fetal Brain Male	brain
23	chr5:90090400-90090800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:90090400-90090800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell

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