Variant report

Variant	rs2438377
Chromosome Location	chr5:90118205-90118206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10514337	0.81[ASN][1000 genomes]
rs11956622	0.86[ASN][1000 genomes]
rs12655163	0.97[ASN][1000 genomes]
rs12655900	0.97[ASN][1000 genomes]
rs12657829	0.95[ASN][1000 genomes]
rs16869112	0.81[ASN][1000 genomes]
rs16869117	0.81[ASN][1000 genomes]
rs16869133	0.83[ASN][1000 genomes]
rs16869139	0.88[ASN][1000 genomes]
rs16869140	0.88[ASN][1000 genomes]
rs16869151	0.90[ASN][1000 genomes]
rs16869163	0.97[ASN][1000 genomes]
rs1983366	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2366932	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2438361	0.88[ASN][1000 genomes]
rs2438366	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2438375	0.86[ASN][1000 genomes]
rs2438379	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2443076	0.83[ASN][1000 genomes]
rs2443084	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3107223	0.83[ASN][1000 genomes]
rs3763073	0.97[ASN][1000 genomes]
rs4916691	0.82[ASN][1000 genomes]
rs7735712	0.93[ASN][1000 genomes]
rs879571	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90092400-90122200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:90100600-90119200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:90103000-90140800	Weak transcription	Brain Germinal Matrix	brain
4	chr5:90104600-90142000	Weak transcription	Brain Anterior Caudate	brain
5	chr5:90106800-90128400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:90110200-90149600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:90112000-90125200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:90112000-90132800	Weak transcription	K562	blood
9	chr5:90112000-90151200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:90112000-90160600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:90112000-90175800	Weak transcription	Fetal Brain Female	brain
12	chr5:90112200-90118800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:90112200-90119000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:90112200-90119000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:90112200-90119000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:90112200-90119000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:90112200-90124800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:90112200-90142200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:90117200-90119800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:90118200-90125400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:90118200-90128600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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