Variant report

Variant	rs11188724
Chromosome Location	chr10:98104703-98104704
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	chr10:98104317..98106846-chr10:98113043..98115259,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10218881	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748671	0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10786280	1.00[ASN][1000 genomes]
rs10882772	0.81[CEU][hapmap]
rs10882775	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882779	0.80[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10882781	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11188722	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs11188726	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188731	0.85[JPT][hapmap]
rs11591467	0.81[CEU][hapmap]
rs11593074	0.81[CEU][hapmap]
rs11597348	0.81[CEU][hapmap]
rs12242936	0.81[JPT][hapmap];0.82[LWK][hapmap]
rs12253096	1.00[YRI][hapmap]
rs12254238	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258764	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs12570008	0.81[JPT][hapmap]
rs12571241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12572329	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17111736	0.81[JPT][hapmap]
rs1923704	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923706	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146390	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs2146392	0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2146393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273891	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs2861572	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2861574	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789938	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs3814224	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818313	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs4424609	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917732	0.80[CEU][hapmap]
rs7077344	0.81[CEU][hapmap]
rs7085949	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096643	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv831950	chr10:98080972-98245434	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11188724	SFRP5	cis	cerebellum	SCAN
rs11188724	CHUK	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98100800-98105000	Strong transcription	Thymus	Thymus
2	chr10:98101400-98105600	Weak transcription	Brain Anterior Caudate	brain
3	chr10:98101400-98105600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr10:98101600-98104800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:98101600-98104800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr10:98101600-98104800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr10:98101600-98104800	Weak transcription	Brain Substantia Nigra	brain
8	chr10:98101600-98105000	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:98101600-98105400	Weak transcription	Brain Angular Gyrus	brain
10	chr10:98101600-98105600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:98101600-98105600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr10:98103600-98105400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:98104000-98106600	ZNF genes & repeats	Dnd41	blood
14	chr10:98104200-98104800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr10:98104200-98105200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:98104200-98105800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr10:98104400-98104800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr10:98104400-98105400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:98104400-98105600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr10:98104400-98105600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr10:98104600-98105800	Enhancers	HUES48 Cell Line	embryonic stem cell

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