Variant report

Variant	rs2443091
Chromosome Location	chr5:90147447-90147448
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12519770	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs13188479	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs2244356	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247546	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2247870	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2438352	0.81[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2438353	0.85[CEU][hapmap]
rs2438355	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap]
rs2438362	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2438364	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2438368	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2443079	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2443085	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2460167	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2443091	GPR98	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90110200-90149600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:90112000-90151200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:90112000-90160600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:90112000-90175800	Weak transcription	Fetal Brain Female	brain
5	chr5:90137400-90148800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:90138000-90148600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:90142400-90149600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:90142400-90156200	Weak transcription	Fetal Brain Male	brain
9	chr5:90142600-90162400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:90144600-90148200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:90145200-90153400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:90145600-90149400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:90145600-90153200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:90146200-90148600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:90146200-90149400	Weak transcription	K562	blood
16	chr5:90146600-90148400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:90146800-90152600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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