Variant report

Variant	rs10060641
Chromosome Location	chr5:90213250-90213251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90205148..90207152-chr5:90211659..90214340,2	MCF-7	breast:
2	chr5:90194213..90195845-chr5:90213067..90215905,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10035662	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10052015	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10052314	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10053303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10059629	0.92[CHB][hapmap]
rs10078496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078568	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs10079044	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10474336	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10514340	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12054681	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]
rs12055217	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12513628	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12515473	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12515481	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12520956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12522395	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13353995	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13355731	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16869175	0.83[CHB][hapmap]
rs16869247	0.83[ASN][1000 genomes]
rs17556421	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[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];0.94[ASN][1000 genomes]
rs4916827	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs4916829	0.83[CHB][hapmap];0.93[CHD][hapmap];0.80[TSI][hapmap]
rs55977992	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56908576	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57954532	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58201771	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6878896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73185149	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73185150	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7724016	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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
rs10060641	C5orf36	cis	parietal	SCAN

Chromatin state (count:21 , 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	chr5:90205200-90217600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:90205200-90219200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:90208000-90231000	Weak transcription	Brain Anterior Caudate	brain
7	chr5:90208200-90213400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:90208600-90217400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:90211400-90217600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:90211600-90225000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:90211600-90225000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:90212000-90215000	Enhancers	Liver	Liver
13	chr5:90212600-90213600	Enhancers	HepG2	liver
14	chr5:90212800-90214200	Enhancers	Fetal Kidney	kidney
15	chr5:90213000-90213600	Enhancers	A549	lung
16	chr5:90213000-90214000	Enhancers	HUVEC	blood vessel
17	chr5:90213000-90215200	Enhancers	Hela-S3	cervix
18	chr5:90213200-90213400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:90213200-90215200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:90213200-90215200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:90213200-90216000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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