Variant report

Variant	rs11604642
Chromosome Location	chr11:71222355-71222356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr11:71222255-71222923	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71214508..71217959-chr11:71220127..71223025,3	MCF-7	breast:
2	chr11:71221136..71223101-chr11:71257935..71260917,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254924	TF binding region
ENSG00000172890	Chromatin interaction
ENSG00000254924	Chromatin interaction
ENSG00000254997	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1044482	0.84[ASN][1000 genomes]
rs11233746	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11233747	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11233789	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11546509	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11600569	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11600860	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11603330	0.84[ASN][1000 genomes]
rs11606033	0.81[ASN][1000 genomes]
rs11606612	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11606631	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12278461	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12419279	0.85[ASN][1000 genomes]
rs12419334	0.85[ASN][1000 genomes]
rs12422045	0.84[ASN][1000 genomes]
rs12785878	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12789751	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12790010	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12790558	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12791871	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12792306	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12793224	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12793530	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12794668	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12797951	0.86[ASN][1000 genomes]
rs12800438	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12806844	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12807718	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12807827	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12808368	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981412	0.84[ASN][1000 genomes]
rs2002063	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2040323	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276360	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276361	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276362	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282620	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2282621	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28364617	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2852853	0.83[ASN][1000 genomes]
rs3794060	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4423214	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4488226	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944062	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944946	0.87[ASN][1000 genomes]
rs4944949	0.87[ASN][1000 genomes]
rs4944955	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944956	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944958	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944959	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944996	0.92[ASN][1000 genomes]
rs4945008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732934	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928249	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7935125	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7938885	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7944926	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs909217	0.86[ASN][1000 genomes]
rs9705153	0.84[AMR][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	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
3	nsv468632	chr11:71200320-71289089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv555402	chr11:71200320-71289089	Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11604642	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs11604642	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11604642	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs11604642	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs11604642	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs11604642	RP11-660L16.2	cis	Stomach	GTEx
rs11604642	RP11-660L16.2	cis	Thyroid	GTEx
rs11604642	RP11-660L16.2	cis	Artery Aorta	GTEx
rs11604642	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs11604642	NADSYN1	cis	lung	GTEx
rs11604642	NADSYN1	cis	Nerve Tibial	GTEx
rs11604642	RP11-660L16.2	cis	Whole Blood	GTEx
rs11604642	NADSYN1	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71211800-71232400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr11:71213200-71232200	Weak transcription	Brain Angular Gyrus	brain
3	chr11:71215000-71222400	Weak transcription	HSMM	muscle
4	chr11:71215600-71236600	Weak transcription	Brain Anterior Caudate	brain
5	chr11:71216400-71235400	Weak transcription	Brain Substantia Nigra	brain
6	chr11:71222000-71230400	Weak transcription	HSMMtube	muscle
7	chr11:71222200-71222400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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