Variant report

Variant	rs734953
Chromosome Location	chr11:101637206-101637207
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	chr11:101635429..101638102-chr11:101641064..101643321,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANGPTL5-1	chr11:101636666-101637899	NONHSAT023862

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1006330	0.90[AMR][1000 genomes]
rs10791521	0.91[ASN][1000 genomes]
rs10791522	0.91[ASN][1000 genomes]
rs10895196	0.91[ASN][1000 genomes]
rs10895197	0.91[ASN][1000 genomes]
rs10895198	0.87[ASN][1000 genomes]
rs10895199	0.84[ASN][1000 genomes]
rs11224994	0.87[AMR][1000 genomes]
rs11224995	0.83[AMR][1000 genomes]
rs11225006	0.82[ASN][1000 genomes]
rs11225009	0.80[ASN][1000 genomes]
rs11225014	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11599998	0.83[ASN][1000 genomes]
rs12361399	0.83[AMR][1000 genomes]
rs12361929	0.81[AMR][1000 genomes]
rs17746310	0.92[AMR][1000 genomes]
rs1939025	0.91[ASN][1000 genomes]
rs1939039	0.83[ASN][1000 genomes]
rs1939043	0.82[AMR][1000 genomes]
rs1939046	0.83[AMR][1000 genomes]
rs1939057	0.80[ASN][1000 genomes]
rs1939064	0.83[AMR][1000 genomes]
rs1939071	0.93[ASN][1000 genomes]
rs1939072	0.90[AMR][1000 genomes]
rs1939073	0.93[ASN][1000 genomes]
rs1939437	0.93[ASN][1000 genomes]
rs1939458	0.85[MEX][hapmap]
rs1939459	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939460	0.92[AMR][1000 genomes]
rs1954767	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105613	0.88[AMR][1000 genomes]
rs2105614	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155057	0.93[ASN][1000 genomes]
rs2155058	0.93[ASN][1000 genomes]
rs2155060	0.90[AMR][1000 genomes]
rs2155061	0.94[ASN][1000 genomes]
rs2155062	0.90[AMR][1000 genomes]
rs2186609	0.90[AMR][1000 genomes]
rs2186610	0.94[ASN][1000 genomes]
rs3920965	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3920966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754022	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4754790	0.83[AMR][1000 genomes]
rs4754791	0.85[AMR][1000 genomes]
rs56245539	0.83[AMR][1000 genomes]
rs60832378	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61916463	0.89[AMR][1000 genomes]
rs6590918	0.90[ASN][1000 genomes]
rs7104516	0.82[ASN][1000 genomes]
rs7105933	0.90[AMR][1000 genomes]
rs7126538	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7131271	0.82[ASN][1000 genomes]
rs732086	0.94[ASN][1000 genomes]
rs732088	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924364	0.87[ASN][1000 genomes]
rs7929894	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898330	chr11:101243644-101722031	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1052159	chr11:101439655-101853293	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1051457	chr11:101446705-101837650	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv530645	chr11:101451416-101778666	Bivalent/Poised TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv898332	chr11:101562004-101732566	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv832249	chr11:101571819-101749073	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv832250	chr11:101617934-101804020	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv430425	chr11:101626575-101741691	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs734953	ARHGAP42	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101635000-101639600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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