Variant report

Variant	rs2438353
Chromosome Location	chr5:90066246-90066247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10045071	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs10052015	0.92[CHB][hapmap]
rs10053303	0.92[CHB][hapmap]
rs10059629	1.00[CHB][hapmap]
rs10060641	0.92[CHB][hapmap]
rs10075623	0.86[ASN][1000 genomes]
rs10078496	0.92[CHB][hapmap]
rs10474336	0.83[CHB][hapmap]
rs10514339	0.87[CHD][hapmap]
rs10514340	0.84[CHB][hapmap]
rs12054681	0.92[CHB][hapmap]
rs12519770	0.88[CEU][hapmap]
rs12520956	0.91[CHB][hapmap]
rs12522395	0.84[CHB][hapmap]
rs13188479	0.89[CEU][hapmap]
rs16869175	0.92[CHB][hapmap];0.87[CHD][hapmap]
rs2049009	0.84[ASN][1000 genomes]
rs2139191	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247415	1.00[CHB][hapmap]
rs2366935	1.00[CHB][hapmap]
rs2438338	0.92[CHB][hapmap]
rs2438342	0.92[CHB][hapmap]
rs2438343	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs2438344	1.00[CHB][hapmap]
rs2438345	0.92[CHB][hapmap];0.84[CHD][hapmap]
rs2438351	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2438352	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2438355	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs2438368	0.82[EUR][1000 genomes]
rs2443068	0.92[CHB][hapmap];0.81[CHD][hapmap]
rs2443079	0.89[CEU][hapmap]
rs2443085	0.84[CEU][hapmap]
rs2443091	0.85[CEU][hapmap]
rs2460167	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs3098356	0.92[CHB][hapmap];0.84[CHD][hapmap]
rs4916698	0.92[CHB][hapmap]
rs4916827	0.92[CHB][hapmap];0.84[CHD][hapmap]
rs4916829	0.92[CHB][hapmap];0.84[CHD][hapmap]
rs6878896	0.92[CHB][hapmap]
rs6890101	0.86[ASN][1000 genomes]
rs7724016	0.92[CHB][hapmap]
rs881289	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2438353	GPR98	cis	cerebellum	SCAN
rs2438353	MEF2C	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90022400-90074000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:90039800-90082000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:90043600-90086800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:90045600-90073000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:90048400-90089200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:90048600-90068600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:90051800-90105000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:90058600-90066400	Strong transcription	K562	blood
9	chr5:90058600-90066800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:90060600-90074200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:90061200-90090800	Weak transcription	Brain Anterior Caudate	brain
12	chr5:90062400-90066400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:90062400-90067800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:90065000-90087000	Weak transcription	Fetal Brain Female	brain
15	chr5:90065400-90069400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:90065800-90066400	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr5:90065800-90071000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:90066000-90073800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:90066200-90066600	Weak transcription	Pancreas	Pancrea
20	chr5:90066200-90073800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:90066200-90087000	Weak transcription	Brain Germinal Matrix	brain
22	chr5:90066200-90089800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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