Variant report

Variant	rs11117745
Chromosome Location	chr1:217173648-217173649
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:217167662..217170376-chr1:217171384..217173746,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10492957	0.81[GIH][hapmap]
rs10779288	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863285	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863286	0.83[YRI][hapmap]
rs11117739	0.85[ASN][1000 genomes]
rs11117740	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11117741	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1339219	0.98[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1339221	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs2576227	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2576228	0.85[ASN][1000 genomes]
rs2576229	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2576230	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2818765	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2818789	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2818790	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2818791	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2818792	0.85[ASN][1000 genomes]
rs2818793	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2818794	0.85[ASN][1000 genomes]
rs2818795	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2818797	0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2818799	0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2818800	0.85[ASN][1000 genomes]
rs3098286	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3098287	0.95[JPT][hapmap];0.85[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	nsv468149	chr1:217134966-217203091	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv549204	chr1:217134966-217203091	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1008670	chr1:217155114-217206765	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1012243	chr1:217157000-217206765	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1006155	chr1:217157000-217215465	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1004880	chr1:217157748-217206765	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1011212	chr1:217162443-217206765	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11117745	LQK1	cis	cerebellum	SCAN
rs11117745	ANGEL2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217157400-217194400	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:217173600-217174200	Enhancers	Left Ventricle	heart
3	chr1:217173600-217187600	Weak transcription	Fetal Heart	heart

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