Variant report

Variant	rs12054681
Chromosome Location	chr5:90217927-90217928
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90213363..90215563-chr5:90217273..90219030,2	MCF-7	breast:
2	chr5:90217916..90220914-chr5:90395407..90397788,2	MCF-7	breast:
3	chr5:90215673..90217953-chr5:90675761..90678552,2	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10035662	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10052015	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10052314	0.83[ASN][1000 genomes]
rs10053303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs10059629	0.92[CHB][hapmap]
rs10060641	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078496	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078568	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs10079044	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10474336	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10514340	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12055217	0.94[ASN][1000 genomes]
rs12513628	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12515473	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12515481	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12520956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12522395	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13353995	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13355731	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16869175	0.83[CHB][hapmap]
rs16869247	0.83[ASN][1000 genomes]
rs17556421	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247415	0.92[CHB][hapmap]
rs2366935	0.91[CHB][hapmap]
rs2438338	0.83[CHB][hapmap]
rs2438342	0.83[CHB][hapmap]
rs2438343	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2438344	0.92[CHB][hapmap]
rs2438345	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs2438353	0.92[CHB][hapmap]
rs2443068	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs28597697	0.92[ASN][1000 genomes]
rs3098356	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs4916698	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs4916827	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs4916829	0.83[CHB][hapmap];0.93[CHD][hapmap];0.83[TSI][hapmap]
rs55977992	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56908576	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57954532	0.94[ASN][1000 genomes]
rs58201771	0.94[ASN][1000 genomes]
rs6878896	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73185149	0.90[ASN][1000 genomes]
rs73185150	0.94[ASN][1000 genomes]
rs7724016	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
3	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
4	esv2754394	chr5:90181320-90225796	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12054681	C5orf36	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90185000-90226600	Weak transcription	K562	blood
2	chr5:90186400-90218000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:90205000-90225000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:90205200-90219200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:90208000-90231000	Weak transcription	Brain Anterior Caudate	brain
6	chr5:90211600-90225000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:90211600-90225000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:90215800-90225000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:90216000-90218600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:90216000-90225000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:90216800-90218000	Enhancers	Liver	Liver
12	chr5:90216800-90218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:90217400-90218800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:90217600-90218200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:90217600-90218800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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